Index

Symbols

--all-pos seismic-wf command line option --ambindel seismic-relate command line option seismic-wf command line option --barcode-end seismic-demult command line option seismic-wf command line option --barcode-start seismic-demult command line option seismic-wf command line option --batch-size seismic-relate command line option seismic-sim-relate command line option seismic-wf command line option --brotli-level seismic-cluster command line option seismic-mask command line option seismic-relate command line option seismic-sim-relate command line option seismic-wf command line option --bt2-contain seismic-align command line option seismic-wf command line option --bt2-D seismic-align command line option seismic-wf command line option --bt2-discordant seismic-align command line option seismic-wf command line option --bt2-dovetail seismic-align command line option seismic-wf command line option --bt2-dpad seismic-align command line option seismic-wf command line option --bt2-end-to-end seismic-align command line option seismic-wf command line option --bt2-gbar seismic-align command line option seismic-wf command line option --bt2-I seismic-align command line option seismic-wf command line option --bt2-i seismic-align command line option seismic-wf command line option --bt2-L seismic-align command line option seismic-wf command line option --bt2-local seismic-align command line option seismic-wf command line option --bt2-mixed seismic-align command line option seismic-wf command line option --bt2-no-contain seismic-align command line option seismic-wf command line option --bt2-no-discordant seismic-align command line option seismic-wf command line option --bt2-no-dovetail seismic-align command line option seismic-wf command line option --bt2-no-mixed seismic-align command line option seismic-wf command line option --bt2-no-un seismic-align command line option seismic-wf command line option --bt2-orient seismic-align command line option seismic-wf command line option --bt2-R seismic-align command line option seismic-wf command line option --bt2-score-min-e2e seismic-align command line option seismic-wf command line option --bt2-score-min-loc seismic-align command line option seismic-wf command line option --bt2-un seismic-align command line option seismic-wf command line option --bt2-X seismic-align command line option seismic-wf command line option --center-fmean seismic-sim-ends command line option seismic-sim-params command line option seismic-sim-total command line option --center-fvar seismic-sim-ends command line option seismic-sim-params command line option seismic-sim-total command line option --cgroup seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --clip-end3 seismic-relate command line option seismic-wf command line option --clip-end5 seismic-relate command line option seismic-wf command line option --clipped seismic-demult command line option seismic-wf command line option --clust-conc seismic-sim-clusts command line option seismic-sim-params command line option seismic-sim-total command line option --cluster seismic-wf command line option --cluster-abundance-table seismic-cluster command line option seismic-table command line option seismic-wf command line option --cluster-pos-table seismic-cluster command line option seismic-table command line option seismic-wf command line option --color seismic-wf command line option --complement seismic-listpos command line option --comppair seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option --compself seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option --csv seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --ct-file seismic-sim-clusts command line option seismic-sim-ends command line option seismic-sim-muts command line option seismic-sim-params command line option --ct-pos-5 seismic-renumct command line option --demult-off seismic-wf command line option --demult-on seismic-wf command line option --demulti-overwrite seismic-demult command line option seismic-wf command line option --dmfastqx seismic-align command line option seismic-wf command line option --dmfastqy seismic-align command line option seismic-wf command line option --dmfastqz seismic-align command line option seismic-wf command line option --draw seismic-wf command line option --em-runs seismic-cluster command line option seismic-wf command line option --em-thresh seismic-cluster command line option seismic-wf command line option --erase-tmp seismic-align command line option seismic-cluster command line option seismic-demult command line option seismic-fold command line option seismic-mask command line option seismic-relate command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --exact-unbias seismic-mask command line option seismic-wf command line option --export seismic-wf command line option --f1r2-fwd seismic-align command line option seismic-wf command line option --f1r2-rev seismic-align command line option seismic-wf command line option --fastp seismic-align command line option seismic-wf command line option --fastp-3 seismic-align command line option seismic-wf command line option --fastp-5 seismic-align command line option seismic-wf command line option --fastp-adapter-1 seismic-align command line option seismic-wf command line option --fastp-adapter-2 seismic-align command line option seismic-wf command line option --fastp-adapter-fasta seismic-align command line option seismic-wf command line option --fastp-adapter-trimming seismic-align command line option seismic-wf command line option --fastp-detect-adapter-for-pe seismic-align command line option seismic-wf command line option --fastp-m seismic-align command line option seismic-wf command line option --fastp-min-length seismic-align command line option seismic-wf command line option --fastp-poly-g seismic-align command line option seismic-wf command line option --fastp-poly-g-min-len seismic-align command line option seismic-wf command line option --fastp-poly-x seismic-align command line option seismic-wf command line option --fastp-poly-x-min-len seismic-align command line option seismic-wf command line option --fastp-w seismic-align command line option seismic-wf command line option --fastqx seismic-align command line option seismic-demult command line option seismic-wf command line option --fastqy seismic-align command line option seismic-wf command line option --fastqz seismic-align command line option seismic-wf command line option --fold seismic-wf command line option --fold-constraint seismic-fold command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --fold-coords seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --fold-full seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-wf command line option --fold-max seismic-fold command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --fold-md seismic-fold command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --fold-mfe seismic-fold command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --fold-percent seismic-fold command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --fold-primers seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --fold-regions-file seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --fold-sub seismic-fold command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --fold-table seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-wf command line option --fold-temp seismic-fold command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --force seismic-align command line option seismic-cleanfa command line option seismic-cluster command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-listpos command line option seismic-mask command line option seismic-relate command line option seismic-renumct command line option seismic-sim-clusts command line option seismic-sim-ends command line option seismic-sim-fastq command line option seismic-sim-fold command line option seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-ref command line option seismic-sim-relate command line option seismic-sim-total command line option seismic-table command line option seismic-wf command line option --fq-gzip seismic-sim-fastq command line option seismic-sim-total command line option --fq-text seismic-sim-fastq command line option seismic-sim-total command line option --graph-abundance seismic-wf command line option --graph-aucroll seismic-wf command line option --graph-giniroll seismic-wf command line option --graph-mhist seismic-wf command line option --graph-mprof seismic-wf command line option --graph-mutdist seismic-wf command line option --graph-ncov seismic-wf command line option --graph-poscorr seismic-wf command line option --graph-roc seismic-wf command line option --graph-tmprof seismic-wf command line option --hist-bins seismic-graph-histpos command line option seismic-graph-histread command line option seismic-wf command line option --hist-margin seismic-graph-histpos command line option seismic-graph-histread command line option seismic-wf command line option --html seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --index-tolerance seismic-demult command line option seismic-wf command line option --inplace seismic-cleanfa command line option seismic-renumct command line option --insert3 seismic-relate command line option seismic-wf command line option --insert5 seismic-relate command line option seismic-wf command line option --jackpot seismic-cluster command line option seismic-wf command line option --jackpot-conf-level seismic-cluster command line option seismic-wf command line option --keep-del seismic-mask command line option seismic-wf command line option --keep-discontig seismic-mask command line option seismic-wf command line option --keep-gu seismic-mask command line option seismic-wf command line option --keep-ins seismic-mask command line option seismic-wf command line option --keep-tmp seismic-align command line option seismic-cluster command line option seismic-demult command line option seismic-fold command line option seismic-mask command line option seismic-relate command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --length-fmean seismic-sim-ends command line option seismic-sim-params command line option seismic-sim-total command line option --length-fvar seismic-sim-ends command line option seismic-sim-params command line option seismic-sim-total command line option --mask-coords seismic-mask command line option seismic-wf command line option --mask-del seismic-mask command line option seismic-wf command line option --mask-discontig seismic-mask command line option seismic-wf command line option --mask-gu seismic-mask command line option seismic-wf command line option --mask-ins seismic-mask command line option seismic-wf command line option --mask-mut seismic-mask command line option seismic-wf command line option --mask-polya seismic-mask command line option seismic-wf command line option --mask-pos seismic-mask command line option seismic-wf command line option --mask-pos-file seismic-mask command line option seismic-wf command line option --mask-pos-table seismic-mask command line option seismic-table command line option seismic-wf command line option --mask-primers seismic-mask command line option seismic-wf command line option --mask-read seismic-mask command line option seismic-wf command line option --mask-read-file seismic-mask command line option seismic-wf command line option --mask-read-table seismic-mask command line option seismic-table command line option seismic-wf command line option --mask-regions-file seismic-mask command line option seismic-wf command line option --max-clusters seismic-cluster command line option seismic-wf command line option --max-em-iter seismic-cluster command line option seismic-wf command line option --max-fmut-pos seismic-listpos command line option seismic-mask command line option seismic-wf command line option --max-fmut-read seismic-mask command line option seismic-wf command line option --max-jackpot-quotient seismic-cluster command line option seismic-wf command line option --max-loglike-vs-best seismic-cluster command line option seismic-wf command line option --max-marcd-vs-best seismic-cluster command line option seismic-wf command line option --max-mask-iter seismic-mask command line option seismic-wf command line option --max-pearson-run seismic-cluster command line option seismic-wf command line option --max-procs seismic-align command line option seismic-cleanfa command line option seismic-cluster command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-listpos command line option seismic-mask command line option seismic-relate command line option seismic-renumct command line option seismic-sim-clusts command line option seismic-sim-ends command line option seismic-sim-fastq command line option seismic-sim-fold command line option seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-relate command line option seismic-sim-total command line option seismic-table command line option seismic-wf command line option --metric seismic-graph-corroll command line option seismic-graph-scatter command line option --min-clusters seismic-cluster command line option seismic-wf command line option --min-em-iter seismic-cluster command line option seismic-wf command line option --min-finfo-read seismic-mask command line option seismic-wf command line option --min-mapq seismic-align command line option seismic-relate command line option seismic-wf command line option --min-marcd-run seismic-cluster command line option seismic-wf command line option --min-mut-gap seismic-mask command line option seismic-sim-fastq command line option seismic-sim-relate command line option seismic-sim-total command line option seismic-wf command line option --min-ncov-read seismic-mask command line option seismic-wf command line option --min-ninfo-pos seismic-mask command line option seismic-wf command line option --min-pearson-vs-best seismic-cluster command line option seismic-wf command line option --min-phred seismic-relate command line option seismic-wf command line option

--min-reads seismic-align command line option seismic-relate command line option seismic-wf command line option --mismatch-tolerence seismic-demult command line option seismic-wf command line option --mix-strands seismic-align command line option seismic-relate command line option seismic-wf command line option --mutdist-null seismic-wf command line option --no-ambindel seismic-relate command line option seismic-wf command line option --no-cluster seismic-wf command line option --no-cluster-abundance-table seismic-cluster command line option seismic-table command line option seismic-wf command line option --no-cluster-pos-table seismic-cluster command line option seismic-table command line option seismic-wf command line option --no-color seismic-wf command line option --no-complement seismic-listpos command line option --no-comppair seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option --no-compself seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option --no-csv seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --no-draw seismic-wf command line option --no-export seismic-wf command line option --no-fastp seismic-align command line option seismic-wf command line option --no-fastp-3 seismic-align command line option seismic-wf command line option --no-fastp-5 seismic-align command line option seismic-wf command line option --no-fastp-adapter-trimming seismic-align command line option seismic-wf command line option --no-fastp-detect-adapter-for-pe seismic-align command line option seismic-wf command line option --no-fastp-poly-x seismic-align command line option seismic-wf command line option --no-fold seismic-wf command line option --no-force seismic-align command line option seismic-cleanfa command line option seismic-cluster command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-listpos command line option seismic-mask command line option seismic-relate command line option seismic-renumct command line option seismic-sim-clusts command line option seismic-sim-ends command line option seismic-sim-fastq command line option seismic-sim-fold command line option seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-ref command line option seismic-sim-relate command line option seismic-sim-total command line option seismic-table command line option seismic-wf command line option --no-graph-abundance seismic-wf command line option --no-graph-aucroll seismic-wf command line option --no-graph-giniroll seismic-wf command line option --no-graph-mhist seismic-wf command line option --no-graph-mprof seismic-wf command line option --no-graph-mutdist seismic-wf command line option --no-graph-ncov seismic-wf command line option --no-graph-poscorr seismic-wf command line option --no-graph-roc seismic-wf command line option --no-graph-tmprof seismic-wf command line option --no-html seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --no-inplace seismic-cleanfa command line option seismic-renumct command line option --no-jackpot seismic-cluster command line option seismic-wf command line option --no-mask-pos-table seismic-mask command line option seismic-table command line option seismic-wf command line option --no-mask-read-table seismic-mask command line option seismic-table command line option seismic-wf command line option --no-mutdist-null seismic-wf command line option --no-overhangs seismic-relate command line option seismic-wf command line option --no-pdf seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --no-png seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --no-relate-pos-table seismic-relate command line option seismic-table command line option seismic-wf command line option --no-relate-read-table seismic-relate command line option seismic-table command line option seismic-wf command line option --no-svg seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --no-verify-times seismic-cluster command line option seismic-table command line option seismic-wf command line option --no-write-read-names seismic-relate command line option seismic-sim-relate command line option seismic-wf command line option --num-reads seismic-sim-fastq command line option seismic-sim-relate command line option seismic-sim-total command line option --out-dir seismic-align command line option seismic-cleanfa command line option seismic-demult command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option seismic-relate command line option seismic-renumct command line option seismic-wf command line option --overhangs seismic-relate command line option seismic-wf command line option --paired-end seismic-sim-fastq command line option seismic-sim-relate command line option seismic-sim-total command line option --parallel-demultiplexing seismic-demult command line option seismic-wf command line option --param-dir seismic-sim-fastq command line option seismic-sim-relate command line option --pdf seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --phred-enc seismic-align command line option seismic-demult command line option seismic-relate command line option seismic-wf command line option --pmut-paired seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-total command line option --pmut-unpaired seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-total command line option --png seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --primer-gap seismic-mask command line option seismic-wf command line option --profile-name seismic-sim-fastq command line option seismic-sim-fold command line option seismic-sim-relate command line option seismic-sim-total command line option --quantile seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --quick-unbias seismic-mask command line option seismic-wf command line option --quick-unbias-thresh seismic-mask command line option seismic-wf command line option --read-length seismic-sim-fastq command line option seismic-sim-relate command line option seismic-sim-total command line option --ref seismic-sim-ref command line option seismic-sim-total command line option --reflen seismic-sim-ref command line option seismic-sim-total command line option --refs seismic-sim-ref command line option seismic-sim-total command line option --refs-meta seismic-demult command line option seismic-wf command line option --relate-cx seismic-relate command line option seismic-wf command line option --relate-pos-table seismic-relate command line option seismic-table command line option seismic-wf command line option --relate-py seismic-relate command line option seismic-wf command line option --relate-read-table seismic-relate command line option seismic-table command line option seismic-wf command line option --rels seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option --rev-label seismic-align command line option seismic-relate command line option seismic-wf command line option --reverse-fraction seismic-sim-fastq command line option seismic-sim-relate command line option seismic-sim-total command line option --sample seismic-sim-fastq command line option seismic-sim-relate command line option seismic-sim-total command line option --samples-meta seismic-wf command line option --sep-strands seismic-align command line option seismic-relate command line option seismic-wf command line option --sim-dir seismic-sim-fold command line option seismic-sim-ref command line option seismic-sim-total command line option --single-end seismic-sim-fastq command line option seismic-sim-relate command line option seismic-sim-total command line option --stop-best-k seismic-cluster command line option seismic-wf command line option --struct-file seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-wf command line option --struct-num seismic-wf command line option --svg seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option --tmp-pfx seismic-align command line option seismic-cluster command line option seismic-demult command line option seismic-fold command line option seismic-mask command line option seismic-relate command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option --try-all-ks seismic-cluster command line option seismic-wf command line option --unmasked-pos seismic-wf command line option --use-count seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option --use-ratio seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option --verbose seismic-test command line option --verify-times seismic-cluster command line option seismic-table command line option seismic-wf command line option --vmut-paired seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-total command line option --vmut-unpaired seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-total command line option --window seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-wf command line option --winmin seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-wf command line option --write-all-ks seismic-cluster command line option seismic-wf command line option --write-best-k seismic-cluster command line option seismic-wf command line option --write-read-names seismic-relate command line option seismic-sim-relate command line option seismic-wf command line option -3 seismic-relate command line option seismic-wf command line option -5 seismic-relate command line option seismic-wf command line option -c seismic-mask command line option seismic-renumct command line option seismic-sim-clusts command line option seismic-sim-params command line option seismic-sim-total command line option seismic-wf command line option -d seismic-sim-fastq command line option seismic-sim-relate command line option -e seismic-cluster command line option seismic-wf command line option -f seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-roc command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option -i seismic-mask command line option seismic-sim-clusts command line option seismic-sim-ends command line option seismic-sim-muts command line option seismic-sim-params command line option seismic-wf command line option -k seismic-cluster command line option seismic-wf command line option -m seismic-graph-corroll command line option seismic-graph-scatter command line option -N seismic-align command line option seismic-relate command line option seismic-sim-ref command line option seismic-sim-total command line option seismic-wf command line option -n seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-sim-fastq command line option seismic-sim-relate command line option seismic-sim-total command line option seismic-wf command line option -o seismic-align command line option seismic-cleanfa command line option seismic-demult command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-scatter command line option seismic-relate command line option seismic-renumct command line option seismic-sim-fold command line option seismic-sim-ref command line option seismic-sim-total command line option seismic-wf command line option -P seismic-mask command line option seismic-sim-fastq command line option seismic-sim-fold command line option seismic-sim-relate command line option seismic-sim-total command line option seismic-wf command line option -p seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-total command line option -q seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-wf command line option -R seismic-demult command line option seismic-sim-ref command line option seismic-sim-total command line option seismic-wf command line option -r seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-sim-ref command line option seismic-sim-total command line option -S seismic-wf command line option -s seismic-sim-fastq command line option seismic-sim-relate command line option seismic-sim-total command line option -t seismic-align command line option seismic-cluster command line option seismic-demult command line option seismic-fold command line option seismic-mask command line option seismic-relate command line option seismic-sim-fold command line option seismic-sim-total command line option seismic-wf command line option -u seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-total command line option -v seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-total command line option seismic-test command line option -w seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-sim-muts command line option seismic-sim-params command line option seismic-sim-total command line option seismic-wf command line option -X seismic-align command line option seismic-wf command line option -x seismic-align command line option seismic-demult command line option seismic-wf command line option -Y seismic-align command line option seismic-wf command line option -y seismic-align command line option seismic-wf command line option -Z seismic-align command line option seismic-wf command line option -z seismic-align command line option seismic-wf command line option

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__getitem__() (seismicrna.core.seq.xna.XNA method) __hash__() (seismicrna.core.seq.xna.XNA method) __mul__() (seismicrna.core.seq.xna.XNA method) __repr__() (seismicrna.core.seq.xna.XNA method) __setattr__() (seismicrna.core.report.Report method) __str__() (seismicrna.relate.aux.cigarop.CigarOp method)

A

a (seismicrna.core.rel.pattern.HalfRelPattern attribute) ABS_TOL (seismicrna.core.tests.unbias_test.TestQuickUnbias attribute) AbundanceTable (class in seismicrna.core.table.base) AbundanceTableRunner (class in seismicrna.graph.table) AbundanceTableWriter (class in seismicrna.core.table.write) accumulate_batches() (in module seismicrna.core.batch.accum) accumulate_counts() (in module seismicrna.core.batch.accum) ACTION (seismicrna.core.logs.Level attribute) action (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.graph.onesource.OneSourceGraph property) (seismicrna.graph.onetable.OneTableGraph property) action() (seismicrna.core.logs.Logger method) action1 (seismicrna.graph.twotable.TwoTableGraph property) action2 (seismicrna.graph.twotable.TwoTableGraph property) action_sample1 (seismicrna.graph.twotable.TwoTableGraph property) action_sample2 (seismicrna.graph.twotable.TwoTableGraph property) add() (seismicrna.core.seq.refs.RefSeqs method) (seismicrna.relate.py.ambindel.IndelPod method) add_mask() (seismicrna.core.seq.region.Region method) adjust_counts() (in module seismicrna.mask.table) align_samples() (in module seismicrna.align.write) AlignRefReport (class in seismicrna.align.report) AlignReport (class in seismicrna.align.report) AlignSampleReport (class in seismicrna.align.report) all_patterns() (in module seismicrna.core.table.base) allc() (seismicrna.core.rel.pattern.HalfRelPattern class method) (seismicrna.core.rel.pattern.RelPattern class method) alph() (seismicrna.core.seq.xna.DNA class method) (seismicrna.core.seq.xna.RNA class method) (seismicrna.core.seq.xna.XNA class method) Annotation (class in seismicrna.graph.base) annotations (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.scatter.ScatterGraph property) AnsiCode (class in seismicrna.core.logs) any_nan() (in module seismicrna.core.mu.nan) append_files() (in module seismicrna.demult.demultiplex) apply_mask() (in module seismicrna.mask.batch)

args_to_cmd() (in module seismicrna.core.extern.shell) array (seismicrna.core.seq.xna.XNA property) as_fancy() (seismicrna.core.rel.pattern.HalfRelPattern class method) as_list_of_tuples() (in module seismicrna.core.task) as_match() (seismicrna.core.rel.pattern.HalfRelPattern class method) as_plain() (seismicrna.core.rel.pattern.HalfRelPattern class method) as_sam() (in module seismicrna.relate.tests.relate_test) as_str (seismicrna.core.path.Field property) (seismicrna.core.path.Path property) (seismicrna.core.path.Segment property) assemble_log_obs_exp() (in module seismicrna.cluster.obsexp) assert_equal() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsAll method) assert_raise() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) assign_clusterings() (in module seismicrna.cluster.emk) auc (seismicrna.core.rna.state.RNAState property) auto() (in module seismicrna.core.arg.docdef) auto_defaults() (in module seismicrna.core.arg.docdef) auto_docstrs() (in module seismicrna.core.arg.docdef) auto_fields() (seismicrna.align.report.AlignReport class method) (seismicrna.cluster.io.ClusterIO class method) (seismicrna.cluster.report.ClusterReport class method) (seismicrna.cluster.report.JoinClusterReport class method) (seismicrna.core.io.file.FileIO class method) (seismicrna.core.io.seq.RefseqIO class method) (seismicrna.fold.report.FoldReport class method) (seismicrna.mask.io.MaskIO class method) (seismicrna.mask.report.JoinMaskReport class method) (seismicrna.mask.report.MaskReport class method) (seismicrna.relate.io.RelateIO class method) (seismicrna.relate.report.PoolReport class method) auto_reframe() (in module seismicrna.core.mu.frame) auto_remove_nan() (in module seismicrna.core.mu.nan) auto_removes_nan() (in module seismicrna.core.mu.nan) AverageDataset (class in seismicrna.relate.dataset) AverageTable (class in seismicrna.relate.table) AverageTabulator (class in seismicrna.relate.table)

B

BadReferenceNameError BadReferenceNameLineError BaseGraph (class in seismicrna.graph.base) BaseRunner (class in seismicrna.graph.base) BaseWriter (class in seismicrna.graph.base) batch_nums (seismicrna.core.dataset.Dataset property) batch_read_index (seismicrna.core.batch.read.ReadBatch property) batch_types() (seismicrna.core.report.BatchedReport class method) BatchedRefseqReport (class in seismicrna.core.report) BatchedReport (class in seismicrna.core.report) batches() (seismicrna.relate.tests.main_test.TestRelate method) BatchTabulator (class in seismicrna.core.table.write) best_index() (seismicrna.cluster.emk.EMRunsK method) best_k (seismicrna.cluster.dataset.ClusterMutsDataset property) (seismicrna.cluster.dataset.ClusterReadDataset property) (seismicrna.cluster.dataset.JoinClusterMutsDataset property) (seismicrna.core.dataset.Dataset property) (seismicrna.relate.dataset.AverageDataset property) best_struct (seismicrna.draw.draw.RNArtistRun property) bic (seismicrna.cluster.em.EMRun property) BOLD (seismicrna.core.logs.AnsiCode attribute)

bootstrap_jackpot_scores() (in module seismicrna.cluster.jackpot) bowtie2_build_cmd() (in module seismicrna.align.xamops) bowtie2_cmd() (in module seismicrna.align.xamops) BOWTIE2_FLAGS (seismicrna.align.fqunit.FastqUnit attribute) bowtie2_inputs (seismicrna.align.fqunit.FastqUnit property) BrickleIO (class in seismicrna.core.io.file) broadcast_regex() (in module seismicrna.core.mu.tests.frame_test) broadcastable() (in module seismicrna.core.mu.tests.frame_test) btype() (seismicrna.core.io.batch.ReadBatchIO class method) build() (in module seismicrna.core.path) (seismicrna.core.path.Field method) (seismicrna.core.path.Path method) (seismicrna.core.path.Segment method) build_jinja_data() (in module seismicrna.draw.draw) build_path() (seismicrna.core.io.file.FileIO class method) (seismicrna.core.table.base.Table class method) builddir() (in module seismicrna.core.path) buildpar() (in module seismicrna.core.path) by_read() (seismicrna.core.table.base.AbundanceTable class method) (seismicrna.core.table.base.PositionTable class method) (seismicrna.core.table.base.ReadTable class method) (seismicrna.core.table.base.Table class method)

C

c (seismicrna.core.rel.pattern.HalfRelPattern attribute) calc_arcsine_distance() (in module seismicrna.core.mu.compare) calc_beta_mv() (in module seismicrna.core.stats) calc_beta_params() (in module seismicrna.core.stats) calc_coeff_determ() (in module seismicrna.core.mu.compare) calc_confidence_interval() (seismicrna.cluster.tests.jackpot_test.TestBootstrapJackpotScores static method) calc_count_per_pos() (in module seismicrna.core.batch.count) calc_count_per_read() (in module seismicrna.core.batch.count) calc_coverage() (in module seismicrna.core.batch.count) calc_dirichlet_mv() (in module seismicrna.core.stats) calc_dirichlet_params() (in module seismicrna.core.stats) calc_dt_minutes() (in module seismicrna.core.report) calc_extra_threads() (in module seismicrna.core.ngs.xam) calc_flags_sep_strands() (in module seismicrna.align.write) calc_gini() (in module seismicrna.core.mu.measure) calc_inverse() (in module seismicrna.core.array) calc_jackpot_quotient() (in module seismicrna.cluster.jackpot) calc_jackpot_score() (in module seismicrna.cluster.jackpot) calc_jackpot_score_ci() (in module seismicrna.cluster.jackpot) calc_lateral5() (in module seismicrna.relate.py.ambindel) calc_marginal() (in module seismicrna.cluster.marginal) calc_marginal_resps() (in module seismicrna.cluster.marginal) calc_mean_arcsine_distance() (in module seismicrna.core.mu.compare) calc_mean_arcsine_distance_clusters() (in module seismicrna.cluster.emk) calc_mean_pearson_clusters() (in module seismicrna.cluster.emk) calc_min_mut_dist() (seismicrna.core.batch.muts.RegionMutsBatch method) calc_muts_matrix() (in module seismicrna.core.batch.muts) calc_n_reads_per_pos() (in module seismicrna.core.unbias) calc_p_clust() (in module seismicrna.core.unbias) calc_p_clust_given_ends_noclose() (in module seismicrna.core.unbias) calc_p_clust_given_noclose() (in module seismicrna.core.unbias) calc_p_ends() (in module seismicrna.core.unbias) calc_p_ends_given_clust_noclose() (in module seismicrna.core.unbias) calc_p_ends_given_noclose() (in module seismicrna.core.unbias) calc_p_ends_observed() (in module seismicrna.core.unbias) calc_p_mut_given_span() (in module seismicrna.core.unbias) calc_p_mut_given_span_noclose() (in module seismicrna.core.unbias) calc_p_noclose() (in module seismicrna.core.unbias) calc_p_noclose_given_clust() (in module seismicrna.core.unbias) calc_p_noclose_given_ends() (in module seismicrna.core.unbias) calc_p_noclose_given_ends_auto() (in module seismicrna.core.unbias) calc_p_nomut_window() (in module seismicrna.core.unbias) calc_params() (in module seismicrna.core.unbias) calc_params_observed() (in module seismicrna.core.unbias) calc_pearson() (in module seismicrna.core.mu.compare) calc_phi() (in module seismicrna.graph.poscorr) (in module seismicrna.graph.pospair) calc_pmut_pattern() (in module seismicrna.sim.muts) calc_pool_size() (in module seismicrna.core.task) calc_quantile() (in module seismicrna.core.mu.scale) calc_ranks() (in module seismicrna.core.mu.scale) calc_reads_per_pos() (in module seismicrna.core.batch.count) calc_rectangular_sum() (in module seismicrna.core.unbias) calc_ref_region_length() (in module seismicrna.ensembles) calc_regions() (in module seismicrna.ensembles) calc_rels_lines() (in module seismicrna.relate.py.relate) calc_rels_per_pos() (in module seismicrna.core.batch.count) calc_rels_per_read() (in module seismicrna.core.batch.count) calc_semi_g_anomaly() (in module seismicrna.cluster.jackpot) calc_signal_noise() (in module seismicrna.core.mu.measure) calc_spanning_sum_slow() (seismicrna.core.tests.unbias_test.TestCalcRectangularSum static method) calc_spearman() (in module seismicrna.core.mu.compare) calc_sum_arcsine_distance() (in module seismicrna.core.mu.compare) calc_taken() (in module seismicrna.core.report) calc_true() (seismicrna.core.mu.tests.compare_test.TestCalcCoeffDeterm class method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson class method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman class method) CalcRefRegionLengthError cast_path() (in module seismicrna.core.path) cgroup_table() (in module seismicrna.graph.cgroup) check_all_done() (in module seismicrna.demult.demultiplex) check_batch_type() (seismicrna.core.join.JoinMutsDataset class method) check_data_path() (in module seismicrna.fold.rnastructure) check_done() (in module seismicrna.demult.demultiplex) check_duplicates() (in module seismicrna.relate.main) check_exists() (seismicrna.demult.demultiplex.super_fastq method) check_file_extension() (in module seismicrna.core.path) check_fqs_xams() (in module seismicrna.align.write) check_naturals() (in module seismicrna.core.array) check_no_identical() (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs method) check_set() (seismicrna.demult.demultiplex.super_fastq method) CHECKSUM_KEY (seismicrna.mask.write.Masker attribute) ci_count() (seismicrna.core.table.base.PositionTable method) ci_ratio() (seismicrna.core.table.base.PositionTable method) cigar (seismicrna.relate.py.relate.SamRead attribute) CigarOp (class in seismicrna.relate.aux.cigarop) CJOINED (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) clean_fasta() (in module seismicrna.cleanfa.cleanfa) close() (seismicrna.core.logs.FileStream method) clust_params (seismicrna.ensembles.RegionInfo property) cluster() (in module seismicrna.cluster.write) ClusterAbundanceGraph (class in seismicrna.graph.abundance)

ClusterAbundanceRunner (class in seismicrna.graph.abundance) ClusterAbundanceWriter (class in seismicrna.graph.abundance) ClusterBatchIO (class in seismicrna.cluster.io) ClusterBatchWriter (class in seismicrna.cluster.io) ClusterDataset (class in seismicrna.cluster.dataset) ClusterDatasetTabulator (class in seismicrna.cluster.table) clustered() (seismicrna.core.header.ClustHeader class method) (seismicrna.core.header.Header class method) (seismicrna.core.header.RelHeader class method) ClusterGroupGraph (class in seismicrna.graph.cgroup) ClusterGroupRunner (class in seismicrna.graph.cgroup) ClusterIO (class in seismicrna.cluster.io) ClusterMutsBatch (class in seismicrna.cluster.batch) ClusterMutsDataset (class in seismicrna.cluster.dataset) ClusterReadBatch (class in seismicrna.cluster.batch) ClusterReadDataset (class in seismicrna.cluster.dataset) ClusterReport (class in seismicrna.cluster.report) ClustHeader (class in seismicrna.core.header) clusts (seismicrna.cluster.dataset.JoinClusterMutsDataset property) (seismicrna.core.header.ClustHeader property) (seismicrna.core.header.Header property) (seismicrna.core.header.RelHeader property) cmap (seismicrna.graph.color.ColorMapGraph property) cmds_to_pipe() (in module seismicrna.core.extern.shell) cmds_to_series() (in module seismicrna.core.extern.shell) cmds_to_subshell() (in module seismicrna.core.extern.shell) codes (seismicrna.core.rel.pattern.HalfRelPattern property) codestring (seismicrna.graph.rel.MultiRelsGraph property) (seismicrna.graph.rel.OneRelGraph property) (seismicrna.graph.rel.RelGraph property) col_titles (seismicrna.graph.cgroup.ClusterGroupGraph property) col_tracks (seismicrna.graph.abundance.ClusterAbundanceGraph property) (seismicrna.graph.cgroup.ClusterGroupGraph property) (seismicrna.graph.onesource.OneSourceGraph property) (seismicrna.graph.twotable.TwoTableRelClusterGroupGraph property) collate_xam_cmd() (in module seismicrna.core.ngs.xam) color_dict (seismicrna.draw.draw.RNArtistRun property) ColorBlock (class in seismicrna.draw.draw) ColorMap (class in seismicrna.graph.color) ColorMapGraph (class in seismicrna.graph.color) columns (seismicrna.core.table.write.TableWriter property) combine_metadata() (in module seismicrna.export.meta) compare() (seismicrna.cluster.tests.marginal_test.TestMarginalResps method) (seismicrna.core.seq.tests.region_test.TestGetWindows method) (seismicrna.core.tests.unbias_test.TestTriuLog method) (seismicrna.core.tests.unbias_test.TestTriuNorm method) compare_result() (seismicrna.cluster.tests.emk_test.TestAssignClusterings method) compare_windows() (in module seismicrna.core.mu.compare) compile() (seismicrna.core.rel.pattern.HalfRelPattern class method) compress() (seismicrna.core.seq.xna.XNA method) CompressedSeq (class in seismicrna.core.seq.xna) compute_auc() (in module seismicrna.core.rna.roc) compute_auc_roc() (in module seismicrna.core.rna.roc) compute_roc_curve() (in module seismicrna.core.rna.roc) compute_rolling_auc() (in module seismicrna.core.rna.roc) conform_series() (in module seismicrna.export.web) ConnectivityTableAlreadyRetitledError console_stream (seismicrna.core.logs.Logger attribute) ConsoleStream (class in seismicrna.core.logs) content (seismicrna.core.logs.Message attribute) contiguous (seismicrna.core.batch.ends.EndCoords property) coord (seismicrna.core.seq.region.Region property) copy() (seismicrna.core.seq.region.Region method) count (seismicrna.core.seq.region.RefRegions property) count_all() (seismicrna.core.batch.muts.RegionMutsBatch method) count_base_types() (in module seismicrna.core.batch.index) count_cigar_muts() (in module seismicrna.relate.aux.cigarop) count_cigar_read() (in module seismicrna.relate.aux.cigarop) count_cigar_ref() (in module seismicrna.relate.aux.cigarop) count_end_coords() (in module seismicrna.core.batch.count) count_fastq_reads() (in module seismicrna.align.fqunit) count_per_pos() (seismicrna.core.batch.muts.RegionMutsBatch method) count_per_read() (seismicrna.core.batch.muts.RegionMutsBatch method) count_pos() (in module seismicrna.core.mu.dim) count_reads() (seismicrna.cluster.tests.jackpot_test.TestSimReads static method) count_reads_segments() (in module seismicrna.core.batch.ends) count_single_paired() (in module seismicrna.core.ngs.xam) count_total_reads() (in module seismicrna.core.ngs.xam) counts_per_pos (seismicrna.core.table.write.Tabulator property) counts_per_read (seismicrna.core.table.write.Tabulator property) counts_pos() (in module seismicrna.core.mu.dim) counts_pos_consensus() (in module seismicrna.core.mu.dim) CountTabulator (class in seismicrna.core.table.write) cover_per_pos (seismicrna.core.batch.muts.RegionMutsBatch property) cover_per_read (seismicrna.core.batch.muts.RegionMutsBatch property) create_path_type() (in module seismicrna.core.path) create_report() (in module seismicrna.demult.demultiplex) (seismicrna.mask.write.Masker method) create_tmp_sam() (seismicrna.relate.sam.XamViewer method) ct_data (seismicrna.core.rna.struct.RNAStructure property) ct_text (seismicrna.core.rna.struct.RNAStructure property) ct_title (seismicrna.core.rna.struct.RNAStructure property) ct_to_db() (in module seismicrna.core.rna.io)

D

data (seismicrna.core.table.base.AbundanceTable property) (seismicrna.core.table.base.RelTypeTable property) (seismicrna.core.table.base.Table property) (seismicrna.core.table.write.AbundanceTableWriter property) (seismicrna.core.table.write.PositionTableWriter property) (seismicrna.core.table.write.ReadTableWriter property) (seismicrna.graph.abundance.ClusterAbundanceGraph property) (seismicrna.graph.aucroll.RollingAUCGraph property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.hist.HistogramGraph property) (seismicrna.graph.mutdist.MutationDistanceGraph property) (seismicrna.graph.pospair.PositionPairGraph property) (seismicrna.graph.profile.ProfileGraph property) (seismicrna.graph.roc.ROCGraph property) (seismicrna.graph.scatter.ScatterGraph property) (seismicrna.graph.statroll.RollingStatGraph property) (seismicrna.graph.twotable.TwoTableMergedClusterGroupGraph property) (seismicrna.relate.table.RelTypeTableLoader property) data1 (seismicrna.graph.twotable.TwoTableRelClusterGroupGraph property) data2 (seismicrna.graph.twotable.TwoTableRelClusterGroupGraph property) data_dirs (seismicrna.core.dataset.Dataset property) (seismicrna.core.dataset.LoadedDataset property) (seismicrna.core.dataset.MergedDataset property) (seismicrna.core.dataset.MultistepDataset property) data_header (seismicrna.graph.hist.HistogramGraph property) (seismicrna.graph.profile.ProfileGraph property) data_kind (seismicrna.graph.table.TableGraph property) data_per_clust (seismicrna.core.table.write.Tabulator property) (seismicrna.relate.table.AverageTabulator property) data_per_pos (seismicrna.core.table.write.Tabulator property) (seismicrna.mask.table.PartialTabulator property) data_per_read (seismicrna.core.table.write.Tabulator property) Dataset (class in seismicrna.core.dataset) dataset() (seismicrna.mask.tests.main_test.TestMask method) dataset_types() (seismicrna.core.table.write.DatasetTabulator class method) DatasetGraph (class in seismicrna.graph.dataset) DatasetRunner (class in seismicrna.graph.dataset) datasets (seismicrna.core.dataset.MergedDataset property) (seismicrna.core.dataset.TallDataset property) (seismicrna.core.dataset.WideDataset property) DatasetTabulator (class in seismicrna.core.table.write) DatasetWriter (class in seismicrna.graph.dataset) db_structure (seismicrna.core.rna.struct.RNAStructure property) db_title (seismicrna.core.rna.struct.RNAStructure property) db_to_ct() (in module seismicrna.core.rna.io) decode_phred() (in module seismicrna.core.ngs.phred) decompile() (seismicrna.core.rel.pattern.HalfRelPattern class method)

decompress() (in module seismicrna.core.seq.xna) (seismicrna.core.seq.xna.CompressedSeq method) deduplicate() (in module seismicrna.core.path) deduplicate_rels() (in module seismicrna.core.header) deduplicated() (in module seismicrna.core.path) default (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) default_key() (in module seismicrna.core.report) default_path_fields() (seismicrna.core.table.base.Table class method) delete_sam() (in module seismicrna.relate.tests.sam_test) delete_tmp_sam() (seismicrna.relate.sam.XamViewer method) Deletion (class in seismicrna.relate.py.ambindel) DeletionPod (class in seismicrna.relate.py.ambindel) DeltaProfileGraph (class in seismicrna.graph.delprof) DeltaProfileRunner (class in seismicrna.graph.delprof) DeltaProfileWriter (class in seismicrna.graph.delprof) demultiplex_run() (in module seismicrna.demult.demultiplex) dependency_exists() (in module seismicrna.core.extern.depend) DependencyError destroy_temp_data() (seismicrna.demult.demultiplex.super_fastq method) DETAIL (seismicrna.core.logs.Level attribute) detail() (seismicrna.core.logs.Logger method) details (seismicrna.graph.abundance.ClusterAbundanceGraph property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.corroll.RollingCorrelationGraph property) (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.graph.roll.RollingGraph property) (seismicrna.graph.table.RelTableGraph property) dict (seismicrna.core.rna.struct.RNAStructure property) (seismicrna.core.seq.region.RefRegions property) dict_to_pairs() (in module seismicrna.core.rna.pair) dict_to_table() (in module seismicrna.core.rna.pair) digest_data() (in module seismicrna.core.io.brickle) digest_file() (in module seismicrna.core.io.brickle) dir (seismicrna.core.dataset.Dataset property) dir_seg_types() (seismicrna.align.report.AlignReport class method) (seismicrna.core.io.file.FileIO class method) (seismicrna.core.io.file.RefIO class method) (seismicrna.core.io.file.RegIO class method) (seismicrna.fold.report.FoldReport class method) dispatch() (in module seismicrna.core.task) DNA (class in seismicrna.core.seq.xna) draw() (in module seismicrna.draw.draw) dtype (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) DuplicateReferenceNameError DuplicateSampleReferenceError

E

edited_numbers (seismicrna.draw.draw.RNArtistRun property) EMRun (class in seismicrna.cluster.em) EMRunsK (class in seismicrna.cluster.emk) encode_phred() (in module seismicrna.core.ngs.phred) encode_relate() (in module seismicrna.relate.py.encode) END (seismicrna.core.logs.AnsiCode attribute) end3 (seismicrna.core.rna.base.RNARegion property) (seismicrna.core.table.base.PositionTable property) end3s() (seismicrna.mask.tests.main_test.TestMask class method) (seismicrna.mask.tests.main_test.TestMaskPaired class method) (seismicrna.mask.tests.main_test.TestMaskSingle class method) end5 (seismicrna.core.rna.base.RNARegion property) (seismicrna.core.table.base.PositionTable property) end5s() (seismicrna.mask.tests.main_test.TestMask class method) (seismicrna.mask.tests.main_test.TestMaskPaired class method) (seismicrna.mask.tests.main_test.TestMaskSingle class method) end_counts (seismicrna.core.table.write.Tabulator property) EndCoords (class in seismicrna.core.batch.ends) ends (seismicrna.ensembles.RegionInfo property)

enough_runs_passing() (seismicrna.cluster.emk.EMRunsK method) ensure_order() (in module seismicrna.core.array) ensure_same_length() (in module seismicrna.core.array) equate() (seismicrna.sim.tests.ends_test.TestSimPEnds method) erase_config() (in module seismicrna.core.logs) ERROR (seismicrna.core.logs.Level attribute) error() (seismicrna.core.logs.Logger method) evaluate() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) exc_info() (in module seismicrna.core.logs) expand_degenerate_seq() (in module seismicrna.core.seq.xna) export_cmd() (in module seismicrna.align.xamops) export_sample() (in module seismicrna.export.web) ext() (seismicrna.core.table.base.Table class method) ext_type (seismicrna.core.path.Segment property) extract_batches() (in module seismicrna.relate.tests.main_test) extract_fasta_seqname() (in module seismicrna.core.seq.fasta) extract_positions() (in module seismicrna.mask.tests.main_test) extract_read_nums() (in module seismicrna.mask.tests.main_test) extract_reference() (in module seismicrna.align.write) exts (seismicrna.core.path.Segment property)

F

FailedToLoadDatasetError FASTA seismic-align command line option seismic-demult command line option seismic-relate command line option seismic-sim-fold command line option seismic-wf command line option FastaCleaner (class in seismicrna.cleanfa.cleanfa) fastp_cmd() (in module seismicrna.align.xamops) fastq_gz() (in module seismicrna.align.fqunit) fastq_to_dict() (seismicrna.demult.demultiplex.super_fastq method) FastqUnit (class in seismicrna.align.fqunit) FATAL (seismicrna.core.logs.Level attribute) fatal() (seismicrna.core.logs.Logger method) fetch_count() (seismicrna.core.table.base.RelTypeTable method) fetch_ratio() (seismicrna.core.table.base.RelTypeTable method) Field (class in seismicrna.core.path) (class in seismicrna.core.report) field_keys() (in module seismicrna.core.report) (seismicrna.core.report.Report class method) field_titles() (in module seismicrna.core.report) fields() (in module seismicrna.core.report) (seismicrna.align.fqunit.FastqUnit method) (seismicrna.align.report.AlignRefReport class method) (seismicrna.align.report.AlignReport class method) (seismicrna.align.report.AlignSampleReport class method) (seismicrna.cluster.report.ClusterReport class method) (seismicrna.cluster.report.JoinClusterReport class method) (seismicrna.core.report.BatchedReport class method) (seismicrna.core.report.RefseqReport class method) (seismicrna.core.report.Report class method) (seismicrna.fold.report.FoldReport class method) (seismicrna.mask.report.JoinMaskReport class method) (seismicrna.mask.report.MaskReport class method) (seismicrna.relate.report.PoolReport class method) (seismicrna.relate.report.RelateReport class method) figure (seismicrna.graph.base.BaseGraph property) file_path (seismicrna.core.logs.FileStream attribute) file_seg_type() (seismicrna.align.report.AlignRefReport class method) (seismicrna.align.report.AlignSampleReport class method) (seismicrna.cluster.io.ClusterBatchIO class method) (seismicrna.cluster.report.ClusterReport class method) (seismicrna.cluster.report.JoinClusterReport class method) (seismicrna.core.io.file.FileIO class method) (seismicrna.core.io.seq.RefseqIO class method) (seismicrna.fold.report.FoldReport class method) (seismicrna.mask.io.MaskBatchIO class method) (seismicrna.mask.report.JoinMaskReport class method) (seismicrna.mask.report.MaskReport class method) (seismicrna.relate.io.ReadNamesBatchIO class method) (seismicrna.relate.io.RelateBatchIO class method) (seismicrna.relate.report.PoolReport class method) (seismicrna.relate.report.RelateReport class method) file_stream (seismicrna.core.logs.Logger attribute) FileIO (class in seismicrna.core.io.file) FileStream (class in seismicrna.core.logs) fill_whitespace() (in module seismicrna.core.path) Filterer (class in seismicrna.core.logs) filterer (seismicrna.core.logs.ConsoleStream attribute) (seismicrna.core.logs.Stream attribute) find_ambindels() (in module seismicrna.relate.py.ambindel) find_and_replace() (in module seismicrna.migrate) find_best_k() (in module seismicrna.cluster.emk) find_cigar_op_pos_read() (in module seismicrna.relate.aux.cigarop) find_cigar_op_pos_ref() (in module seismicrna.relate.aux.cigarop) find_contiguous_reads() (in module seismicrna.core.batch.ends) find_ct_files() (in module seismicrna.fold.load) find_ct_region() (in module seismicrna.core.rna.io) find_dims() (in module seismicrna.core.array) find_enclosing_pairs() (in module seismicrna.core.rna.pair) find_files() (in module seismicrna.core.path)

find_files_chain() (in module seismicrna.core.path) find_pos() (in module seismicrna.lists.listpos) find_read_end3s() (in module seismicrna.core.batch.ends) find_read_end5s() (in module seismicrna.core.batch.ends) find_root_pairs() (in module seismicrna.core.rna.pair) find_tables() (seismicrna.relate.table.TableLoader class method) finds_multigrepped_reads() (in module seismicrna.demult.demultiplex) fit_uint_size() (in module seismicrna.core.types) fit_uint_type() (in module seismicrna.core.types) fits() (seismicrna.core.rel.pattern.HalfRelPattern method) (seismicrna.core.rel.pattern.RelPattern method) flag (seismicrna.relate.py.relate.SamFlag attribute) (seismicrna.relate.py.relate.SamRead attribute) flags_cmd() (in module seismicrna.align.xamops) flags_cmds() (in module seismicrna.align.xamops) flagstat_cmd() (in module seismicrna.core.ngs.xam) flagstats (seismicrna.relate.sam.XamViewer property) fmt_fancy (seismicrna.core.rel.pattern.HalfRelPattern attribute) fmt_plain (seismicrna.core.rel.pattern.HalfRelPattern attribute) fold() (in module seismicrna.fold.rnastructure) fold_profile() (in module seismicrna.fold.main) fold_region() (in module seismicrna.fold.main) (in module seismicrna.sim.fold) FoldReport (class in seismicrna.fold.report) format() (seismicrna.core.logs.AnsiCode class method) format_clust_name() (in module seismicrna.core.header) format_clust_names() (in module seismicrna.core.header) format_color() (seismicrna.core.logs.AnsiCode class method) format_console_color() (in module seismicrna.core.logs) format_console_plain() (in module seismicrna.core.logs) format_db_structure() (in module seismicrna.core.rna.db) format_exp_count_col() (in module seismicrna.cluster.obsexp) format_fasta_name_line() (in module seismicrna.core.seq.fasta) format_fasta_record() (in module seismicrna.core.seq.fasta) format_fasta_seq_lines() (in module seismicrna.core.seq.fasta) format_logfile() (in module seismicrna.core.logs) format_metadata() (in module seismicrna.export.web) format_phred_arg() (in module seismicrna.align.fqunit) format_read_name() (in module seismicrna.relate.batch) format_ref_reverse() (in module seismicrna.align.write) format_retitled_ct_line() (in module seismicrna.fold.rnastructure) format_version() (in module seismicrna.core.version) Formatter (class in seismicrna.core.logs) formatter (seismicrna.core.logs.ConsoleStream attribute) (seismicrna.core.logs.Formatter attribute) (seismicrna.core.logs.Stream attribute) four() (seismicrna.core.seq.xna.XNA class method) fpr (seismicrna.graph.roc.ROCGraph property) fq_pipeline() (in module seismicrna.align.write) fqs_pipeline() (in module seismicrna.align.write) from_clusters() (seismicrna.cluster.report.ClusterReport class method) from_counts() (seismicrna.core.rel.pattern.HalfRelPattern class method) (seismicrna.core.rel.pattern.RelPattern class method) from_ct() (in module seismicrna.core.rna.io) from_dataset() (seismicrna.cluster.uniq.UniqReads class method) from_dataset_contig() (seismicrna.cluster.uniq.UniqReads class method) from_db() (in module seismicrna.core.rna.io) from_dict() (seismicrna.core.report.Report class method) from_param_dir() (in module seismicrna.sim.fastq) (in module seismicrna.sim.relate) from_paths() (seismicrna.align.fqunit.FastqUnit class method) from_reads() (in module seismicrna.relate.io) from_report() (in module seismicrna.sim.fastq) from_report_format() (seismicrna.core.rel.pattern.HalfRelPattern class method) from_struct_profile() (seismicrna.core.rna.state.RNAState class method) FullPositionTable (class in seismicrna.relate.table) FullReadBatch (class in seismicrna.relate.batch) FullReadTable (class in seismicrna.relate.table) FullRegionMutsBatch (class in seismicrna.relate.batch) FullTable (class in seismicrna.relate.table) FullTabulator (class in seismicrna.relate.table)

G

g (seismicrna.core.rel.pattern.HalfRelPattern attribute) g_test (seismicrna.graph.mutdist.MutationDistanceGraph property) generate_batch() (in module seismicrna.relate.write) generate_both_strands() (in module seismicrna.relate.strands) generate_fastq() (in module seismicrna.sim.fastq) generate_fastq_record() (in module seismicrna.sim.fastq) generate_regions() (in module seismicrna.ensembles) generate_tables() (seismicrna.core.table.write.Tabulator method) get() (seismicrna.core.seq.refs.RefSeqs method) (seismicrna.graph.color.ColorMap method) get_action_name() (in module seismicrna.graph.base) get_alphaset() (seismicrna.core.seq.xna.XNA class method) get_args_count_fastq_reads() (in module seismicrna.align.fqunit) get_batch() (seismicrna.core.dataset.Dataset method) (seismicrna.core.dataset.LoadedDataset method) (seismicrna.core.dataset.MultistepDataset method) (seismicrna.core.dataset.MutsDataset method) (seismicrna.core.dataset.TallDataset method) (seismicrna.core.dataset.WideDataset method) (seismicrna.relate.dataset.RelateMutsDataset method) get_batch_checksum() (seismicrna.core.dataset.LoadedDataset method) get_batch_count_all() (seismicrna.core.dataset.MutsDataset method) get_batch_count_all_func() (in module seismicrna.core.batch.tests.accum_test) get_batch_path() (seismicrna.core.dataset.LoadedDataset method) get_batch_type() (seismicrna.cluster.dataset.ClusterReadDataset class method) (seismicrna.cluster.dataset.JoinClusterMutsDataset class method) (seismicrna.core.dataset.LoadedDataset class method) (seismicrna.core.join.JoinMutsDataset class method) (seismicrna.core.report.BatchedReport class method) (seismicrna.mask.dataset.JoinMaskMutsDataset class method) (seismicrna.mask.dataset.MaskReadDataset class method) (seismicrna.relate.dataset.ReadNamesDataset class method) (seismicrna.relate.dataset.RelateMutsDataset class method) get_bounds() (seismicrna.graph.hist.HistogramGraph method) get_bowtie2_index_paths() (in module seismicrna.align.xamops) get_btype_name() (seismicrna.core.dataset.LoadedDataset class method) get_byte_dtype() (in module seismicrna.core.types) get_clust_header() (seismicrna.core.header.Header method) get_clust_params() (in module seismicrna.cluster.dataset) get_cmap() (in module seismicrna.graph.color) get_cmap_type() (seismicrna.graph.color.ColorMapGraph class method) (seismicrna.graph.delprof.DeltaProfileGraph class method) (seismicrna.graph.hist.HistogramGraph class method) (seismicrna.graph.mutdist.MutationDistanceGraph class method) (seismicrna.graph.profile.MultiRelsProfileGraph class method) (seismicrna.graph.profile.OneRelProfileGraph class method) (seismicrna.graph.scatter.ScatterGraph class method) get_colormaps() (in module seismicrna.graph.color) get_common_k() (in module seismicrna.cluster.emk) get_comp() (seismicrna.core.seq.xna.XNA class method) get_comp_func() (in module seismicrna.core.mu.compare) get_comp_method() (in module seismicrna.core.mu.compare) get_comp_name() (in module seismicrna.core.mu.compare) get_comptrans() (seismicrna.core.seq.xna.XNA class method) get_config() (in module seismicrna.core.logs) get_coords_by_ref() (in module seismicrna.core.seq.region) get_cov_matrix() (seismicrna.cluster.uniq.UniqReads method) get_ct_file() (seismicrna.core.rna.profile.RNAProfile method) (seismicrna.draw.draw.RNArtistRun method) get_ct_path() (in module seismicrna.sim.fold) get_dataset1_load_func() (seismicrna.cluster.dataset.ClusterMutsDataset class method) (seismicrna.core.dataset.MultistepDataset class method) (seismicrna.mask.dataset.MaskMutsDataset class method) get_dataset1_report_file() (seismicrna.core.dataset.MultistepDataset class method) get_dataset2_load_func() (seismicrna.core.dataset.MultistepDataset class method) get_dataset2_type() (seismicrna.cluster.dataset.ClusterMutsDataset class method) (seismicrna.core.dataset.MultistepDataset class method) (seismicrna.mask.dataset.MaskMutsDataset class method) get_dataset_flags() (in module seismicrna.table) get_dataset_load_func() (seismicrna.cluster.dataset.JoinClusterMutsDataset class method) (seismicrna.core.dataset.MergedDataset class method) (seismicrna.mask.dataset.JoinMaskMutsDataset class method) (seismicrna.relate.dataset.PoolDataset class method) (seismicrna.relate.dataset.PoolReadNamesDataset class method) get_db_file() (seismicrna.core.rna.profile.RNAProfile method) (seismicrna.draw.draw.RNArtistRun method) get_db_structs() (in module seismicrna.export.web) get_db_text() (seismicrna.core.rna.struct.RNAStructure method) get_default_color() (seismicrna.graph.color.ColorMap method) (seismicrna.graph.color.RelColorMap method) (seismicrna.graph.color.SeqColorMap method) get_dms_file() (seismicrna.core.rna.profile.RNAProfile method) get_docstr_lines() (in module seismicrna.core.arg.docdef) get_dtype() (in module seismicrna.core.types) get_edges() (seismicrna.graph.hist.HistogramGraph method) get_edges_index() (in module seismicrna.graph.hist) get_fasta() (seismicrna.core.rna.profile.RNAProfile method) get_fasta_path() (in module seismicrna.sim.ref) get_fasta_seq() (in module seismicrna.core.seq.fasta) get_field() (seismicrna.core.report.Report method) get_fields_in_seg_types() (in module seismicrna.core.path) get_graph() (seismicrna.graph.abundance.ClusterAbundanceWriter method) (seismicrna.graph.aucroll.RollingAUCWriter method) (seismicrna.graph.dataset.DatasetWriter method) (seismicrna.graph.hist.HistogramWriter method) (seismicrna.graph.mutdist.MutationDistanceWriter method) (seismicrna.graph.onetable.OneTableWriter method) (seismicrna.graph.pospair.PositionPairWriter method) (seismicrna.graph.profile.ProfileWriter method) (seismicrna.graph.roc.ROCWriter method) (seismicrna.graph.statroll.RollingStatWriter method) get_graph_type() (seismicrna.graph.corroll.RollingCorrelationWriter class method) (seismicrna.graph.delprof.DeltaProfileWriter class method) (seismicrna.graph.giniroll.RollingGiniWriter class method) (seismicrna.graph.hist.HistogramWriter class method) (seismicrna.graph.histpos.PositionHistogramWriter class method) (seismicrna.graph.histread.ReadHistogramWriter class method) (seismicrna.graph.scatter.ScatterWriter class method) (seismicrna.graph.snrroll.RollingSNRWriter class method) (seismicrna.graph.statroll.RollingStatWriter class method) (seismicrna.graph.twotable.TwoTableWriter class method) get_hist_trace() (in module seismicrna.graph.trace) get_indel_by_opp() (seismicrna.relate.py.ambindel.IndelPod method) get_input_loader() (seismicrna.graph.base.BaseRunner class method) (seismicrna.graph.dataset.DatasetRunner class method) (seismicrna.graph.onestruct.StructOneTableRunner class method) (seismicrna.graph.table.AbundanceTableRunner class method) (seismicrna.graph.table.PositionTableRunner class method) (seismicrna.graph.table.ReadTableRunner class method) get_ins_rel() (in module seismicrna.relate.py.ambindel) get_ks() (in module seismicrna.graph.cgroup) get_ks_clusts() (in module seismicrna.graph.cgroup) get_lateral() (in module seismicrna.relate.py.ambindel) (seismicrna.relate.py.ambindel.Indel method) get_length() (in module seismicrna.core.array) get_line_trace() (in module seismicrna.graph.trace) get_list_path() (in module seismicrna.lists.lists)

get_mask() (seismicrna.core.seq.region.Region method) get_max_uint() (in module seismicrna.core.types) get_max_value() (in module seismicrna.core.types) get_mut_matrix() (seismicrna.cluster.uniq.UniqReads method) get_non_seq_regex() (in module seismicrna.cleanfa.cleanfa) get_nonalphaset() (seismicrna.core.seq.xna.XNA class method) get_null_name() (in module seismicrna.graph.mutdist) get_null_value() (seismicrna.core.table.write.Tabulator class method) (seismicrna.mask.table.PartialTabulator class method) (seismicrna.relate.table.FullTabulator class method) get_oconv_dict() (in module seismicrna.core.report) get_oconv_dict_list() (in module seismicrna.core.report) get_oconv_float() (in module seismicrna.core.report) get_oconv_list() (in module seismicrna.core.report) get_other_iupac() (seismicrna.core.seq.xna.XNA class method) get_pairwise_position_trace() (in module seismicrna.graph.trace) get_param_default() (in module seismicrna.core.arg.docdef) get_param_dir_fields() (in module seismicrna.sim.relate) get_param_lines() (in module seismicrna.core.arg.docdef) get_path() (seismicrna.core.io.file.FileIO method) (seismicrna.graph.base.BaseGraph method) get_path_fields() (seismicrna.graph.base.BaseGraph method) (seismicrna.graph.onestruct.StructOneTableGraph method) get_path_segs() (seismicrna.graph.base.BaseGraph class method) get_pattern() (in module seismicrna.core.table.base) get_pictrans() (seismicrna.core.seq.xna.XNA class method) get_read_nums() (seismicrna.cluster.io.ClusterBatchWriter method) get_ref_metadata() (in module seismicrna.export.web) get_reg_coords_primers() (in module seismicrna.core.seq.region) get_reg_metadata() (in module seismicrna.export.web) get_rel_header() (seismicrna.core.header.Header method) get_rel_name() (in module seismicrna.core.table.base) get_release_working_dirs() (in module seismicrna.core.tmp) get_report_type() (seismicrna.cluster.dataset.ClusterReadDataset class method) (seismicrna.cluster.dataset.JoinClusterMutsDataset class method) (seismicrna.core.dataset.Dataset class method) (seismicrna.core.dataset.LoadedDataset class method) (seismicrna.core.dataset.MultistepDataset class method) (seismicrna.mask.dataset.JoinMaskMutsDataset class method) (seismicrna.mask.dataset.MaskReadDataset class method) (seismicrna.relate.dataset.PoolDataset class method) (seismicrna.relate.dataset.PoolReadNamesDataset class method) (seismicrna.relate.dataset.ReadNamesDataset class method) (seismicrna.relate.dataset.RelateMutsDataset class method) get_resps() (seismicrna.cluster.em.EMRun method) get_roc_trace() (in module seismicrna.graph.trace) get_rolling_auc_trace() (in module seismicrna.graph.trace) get_sam_data() (seismicrna.relate.tests.main_test.TestRelate class method) (seismicrna.relate.tests.main_test.TestRelateEmpty class method) (seismicrna.relate.tests.main_test.TestRelatePaired class method) (seismicrna.relate.tests.main_test.TestRelateSingle class method) get_sample_data() (in module seismicrna.export.web) get_sample_metadata() (in module seismicrna.export.web) get_sample_ref_exts() (seismicrna.align.fqunit.FastqUnit method) get_script_file() (seismicrna.draw.draw.RNArtistRun method) get_seismicrna_project_dir() (in module seismicrna.core.path) get_seismicrna_source_dir() (in module seismicrna.core.path) get_seq_base_bar_trace() (in module seismicrna.graph.trace) get_seq_base_scatter_trace() (in module seismicrna.graph.trace) get_seq_line_trace() (in module seismicrna.graph.trace) get_seq_stack_bar_trace() (in module seismicrna.graph.trace) get_shared_index() (in module seismicrna.core.seq.region) get_subpattern() (in module seismicrna.core.table.base) get_svg_file() (seismicrna.draw.draw.RNArtistRun method) get_table_data() (in module seismicrna.export.web) get_table_path() (in module seismicrna.cluster.params) get_tabulator_type() (in module seismicrna.table) get_traces() (seismicrna.graph.abundance.ClusterAbundanceGraph method) (seismicrna.graph.aucroll.RollingAUCGraph method) (seismicrna.graph.base.BaseGraph method) (seismicrna.graph.hist.HistogramGraph method) (seismicrna.graph.mutdist.MutationDistanceGraph method) (seismicrna.graph.pospair.PositionPairGraph method) (seismicrna.graph.profile.MultiRelsProfileGraph method) (seismicrna.graph.profile.OneRelProfileGraph method) (seismicrna.graph.roc.ROCGraph method) (seismicrna.graph.scatter.ScatterGraph method) (seismicrna.graph.statroll.RollingStatGraph method) (seismicrna.graph.twotable.TwoTableMergedClusterGroupGraph method) get_uint_dtype() (in module seismicrna.core.types) get_uint_size() (in module seismicrna.core.types) get_uint_type() (in module seismicrna.core.types) get_uniq_reads() (in module seismicrna.cluster.uniq) get_valid_index() (seismicrna.cluster.emk.EMRunsK method) get_varna_color_file() (seismicrna.core.rna.profile.RNAProfile method) (seismicrna.draw.draw.RNArtistRun method) get_writer_type() (seismicrna.graph.abundance.ClusterAbundanceRunner class method) (seismicrna.graph.aucroll.RollingAUCRunner class method) (seismicrna.graph.base.BaseRunner class method) (seismicrna.graph.corroll.RollingCorrelationRunner class method) (seismicrna.graph.dataset.DatasetRunner class method) (seismicrna.graph.delprof.DeltaProfileRunner class method) (seismicrna.graph.giniroll.RollingGiniRunner class method) (seismicrna.graph.histpos.PositionHistogramRunner class method) (seismicrna.graph.histread.ReadHistogramRunner class method) (seismicrna.graph.mutdist.MutationDistanceRunner class method) (seismicrna.graph.poscorr.PositionCorrelationRunner class method) (seismicrna.graph.pospair.PositionPairRunner class method) (seismicrna.graph.profile.ProfileRunner class method) (seismicrna.graph.roc.ROCRunner class method) (seismicrna.graph.scatter.ScatterRunner class method) (seismicrna.graph.snrroll.RollingSNRRunner class method) (seismicrna.graph.table.TableRunner class method) (seismicrna.graph.twotable.TwoTableRunner class method) graph_attr() (in module seismicrna.cluster.summary) graph_attrs() (in module seismicrna.cluster.summary) graph_filename (seismicrna.graph.base.BaseGraph property) graph_kind() (seismicrna.graph.abundance.ClusterAbundanceGraph class method) (seismicrna.graph.aucroll.RollingAUCGraph class method) (seismicrna.graph.base.BaseGraph class method) (seismicrna.graph.corroll.RollingCorrelationGraph class method) (seismicrna.graph.delprof.DeltaProfileGraph class method) (seismicrna.graph.giniroll.RollingGiniGraph class method) (seismicrna.graph.histpos.PositionHistogramGraph class method) (seismicrna.graph.histread.ReadHistogramGraph class method) (seismicrna.graph.mutdist.MutationDistanceGraph class method) (seismicrna.graph.poscorr.PositionCorrelationGraph class method) (seismicrna.graph.profile.ProfileGraph class method) (seismicrna.graph.roc.ROCGraph class method) (seismicrna.graph.scatter.ScatterGraph class method) (seismicrna.graph.snrroll.RollingSNRGraph class method) graph_log_obs_exp() (in module seismicrna.cluster.obsexp) graph_type() (seismicrna.graph.poscorr.PositionCorrelationWriter class method) (seismicrna.graph.pospair.PositionPairWriter class method) grep_both_fastq() (in module seismicrna.demult.demultiplex) group_clusters() (in module seismicrna.ensembles) guess_data_path() (in module seismicrna.fold.rnastructure) gzipped() (seismicrna.core.table.base.Table class method)

H

HalfRelPattern (class in seismicrna.core.rel.pattern) Header (class in seismicrna.core.header) header (seismicrna.core.table.base.Table property) header_depth() (seismicrna.core.table.base.Table class method) header_rows() (seismicrna.core.table.base.RelTypeTable class method) header_type() (seismicrna.core.table.base.Table class method) (seismicrna.relate.table.AverageTable class method)

HistogramGraph (class in seismicrna.graph.hist) HistogramRunner (class in seismicrna.graph.hist) HistogramWriter (class in seismicrna.graph.hist) hists (seismicrna.graph.mutdist.MutationDistanceGraph property) hyphen (seismicrna.core.seq.region.Region property) hyphenate_ends() (in module seismicrna.core.seq.region)

I

iconv (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) iconv_array_int() (in module seismicrna.core.report) iconv_datetime() (in module seismicrna.core.report) iconv_dict_str_dict_int_dict_int_int() (in module seismicrna.core.report) iconv_dict_str_int() (in module seismicrna.core.report) iconv_int_keys() (in module seismicrna.core.report) idxstats_cmd() (in module seismicrna.core.ngs.xam) IncompatibleValuesError InconsistentValueError Indel (class in seismicrna.relate.py.ambindel) indel_type() (seismicrna.relate.py.ambindel.DeletionPod class method) (seismicrna.relate.py.ambindel.IndelPod class method) (seismicrna.relate.py.ambindel.InsertionPod class method) IndelPod (class in seismicrna.relate.py.ambindel) indels (seismicrna.relate.py.ambindel.DeletionPod attribute) (seismicrna.relate.py.ambindel.IndelPod attribute) (seismicrna.relate.py.ambindel.InsertionPod attribute) index (seismicrna.core.header.ClustHeader property) (seismicrna.core.header.Header property) (seismicrna.core.header.RelClustHeader property) (seismicrna.core.header.RelHeader property) index_cols() (seismicrna.core.table.base.Table class method) index_depth() (seismicrna.core.table.base.AbundanceTable class method) (seismicrna.core.table.base.PositionTable class method) (seismicrna.core.table.base.ReadTable class method) (seismicrna.core.table.base.Table class method) index_to_pos() (in module seismicrna.core.seq.region) index_to_seq() (in module seismicrna.core.seq.region) index_xam_cmd() (in module seismicrna.core.ngs.xam) indexes (seismicrna.relate.sam.XamViewer property) infer_read() (in module seismicrna.relate.aux.infer) init_args (seismicrna.core.rna.base.RNARegion property) (seismicrna.core.rna.profile.RNAProfile property) (seismicrna.core.rna.struct.RNAStructure property) init_kws() (seismicrna.cluster.table.ClusterDatasetTabulator class method) (seismicrna.core.table.write.DatasetTabulator class method) (seismicrna.mask.table.PartialDatasetTabulator class method) (seismicrna.relate.table.RelateDatasetTabulator class method) INPUT_PATH seismic-cleanfa command line option seismic-cluster command line option seismic-fold command line option seismic-graph-aucroll command line option seismic-graph-corroll command line option seismic-graph-delprof command line option seismic-graph-histpos command line option seismic-graph-histread command line option seismic-graph-profile command line option seismic-graph-roc command line option seismic-graph-scatter command line option seismic-listpos command line option seismic-mask command line option seismic-relate command line option seismic-sim-fastq command line option seismic-table command line option seismic-wf command line option

Insertion (class in seismicrna.relate.py.ambindel) InsertionPod (class in seismicrna.relate.py.ambindel) intersect() (in module seismicrna.core.seq.region) (seismicrna.core.rel.pattern.HalfRelPattern method) (seismicrna.core.rel.pattern.RelPattern method) InvalidReportFieldKeyError InvalidReportFieldTitleError invert() (seismicrna.core.rel.pattern.RelPattern method) iopaths() (in module seismicrna.core.extern.shell) is_acgt() (in module seismicrna.relate.py.encode) is_dataset_type() (seismicrna.core.dataset.LoadFunction method) is_paired (seismicrna.core.rna.struct.RNAStructure property) iter() (seismicrna.core.seq.refs.RefSeqs method) iter_alignments() (in module seismicrna.relate.aux.iterread) iter_base_types() (in module seismicrna.core.batch.index) iter_batches() (seismicrna.core.dataset.Dataset method) (seismicrna.core.dataset.MutsDataset method) iter_cases() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) iter_cases_insert3() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) iter_clust_indexes() (seismicrna.core.header.ClustHeader method) (seismicrna.core.header.Header method) (seismicrna.core.header.RelHeader method) iter_clust_table_data() (in module seismicrna.export.web) iter_codes() (in module seismicrna.core.rel.tests.pattern_test) iter_graphs() (seismicrna.graph.abundance.ClusterAbundanceWriter method) (seismicrna.graph.base.BaseWriter method) (seismicrna.graph.dataset.DatasetWriter method) (seismicrna.graph.onestruct.StructOneTableWriter method) (seismicrna.graph.onetable.OneTableRelClusterGroupWriter method) (seismicrna.graph.table.TableWriter method) (seismicrna.graph.twotable.TwoTableRelClusterGroupWriter method) iter_hist_traces() (in module seismicrna.graph.trace) iter_line_traces() (in module seismicrna.graph.trace) iter_pos_table_data() (in module seismicrna.export.web) iter_pos_table_series() (in module seismicrna.export.web) iter_pos_table_struct() (in module seismicrna.export.web) iter_profiles() (seismicrna.core.table.base.PositionTable method) (seismicrna.graph.onestruct.StructOneTableGraph method) iter_read_table_data() (in module seismicrna.export.web) iter_reads() (seismicrna.core.batch.muts.RegionMutsBatch method) iter_records() (seismicrna.relate.sam.XamViewer method) iter_relvecs_all() (in module seismicrna.relate.aux.iterrel) iter_relvecs_q53() (in module seismicrna.relate.aux.iterrel) iter_roc_traces() (in module seismicrna.graph.trace) iter_rolling_auc_traces() (in module seismicrna.graph.trace) iter_root_modules() (seismicrna.core.rna.struct.RNAStructure method) iter_seq_base_bar_traces() (in module seismicrna.graph.trace) iter_seq_base_scatter_traces() (in module seismicrna.graph.trace) iter_seq_line_traces() (in module seismicrna.graph.trace) iter_seqbar_stack_traces() (in module seismicrna.graph.trace) iter_stack_bar_traces() (in module seismicrna.graph.trace) iter_states() (seismicrna.graph.onestruct.StructOneTableGraph method) iter_table_data() (in module seismicrna.export.web) iter_table_pairs() (in module seismicrna.graph.twotable) iter_windows() (in module seismicrna.core.seq.region)

J

jackpot_quotient (seismicrna.cluster.em.EMRun property) jackpot_score (seismicrna.cluster.em.EMRun property) JinjaData (class in seismicrna.draw.draw) join_regions() (in module seismicrna.join) JoinClusterMutsDataset (class in seismicrna.cluster.dataset)

JoinClusterReport (class in seismicrna.cluster.report) joined_mask_report_exists() (in module seismicrna.join) JoinMaskMutsDataset (class in seismicrna.mask.dataset) JoinMaskReport (class in seismicrna.mask.report) JoinMutsDataset (class in seismicrna.core.join) JoinReport (class in seismicrna.core.join)

K

key (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) KEY_DINTER (seismicrna.align.fqunit.FastqUnit attribute) KEY_DMATED (seismicrna.align.fqunit.FastqUnit attribute) KEY_DSINGLE (seismicrna.align.fqunit.FastqUnit attribute) KEY_INTER (seismicrna.align.fqunit.FastqUnit attribute) KEY_MATE1 (seismicrna.align.fqunit.FastqUnit attribute) KEY_MATE2 (seismicrna.align.fqunit.FastqUnit attribute) KEY_MATED (seismicrna.align.fqunit.FastqUnit attribute) KEY_SINGLE (seismicrna.align.fqunit.FastqUnit attribute) key_to_title() (in module seismicrna.core.report) kind (seismicrna.align.fqunit.FastqUnit property) kind() (seismicrna.core.table.base.Table class method) (seismicrna.mask.table.MaskTable class method) (seismicrna.relate.dataset.NamesDataset class method) (seismicrna.relate.table.RelateTable class method)

kmers() (seismicrna.core.seq.xna.XNA method) ks (seismicrna.cluster.dataset.ClusterMutsDataset property) (seismicrna.cluster.dataset.ClusterReadDataset property) (seismicrna.cluster.dataset.JoinClusterMutsDataset property) (seismicrna.core.dataset.Dataset property) (seismicrna.core.header.ClustHeader property) (seismicrna.core.header.Header property) (seismicrna.core.header.RelHeader property) (seismicrna.relate.dataset.AverageDataset property) ks_written (seismicrna.cluster.io.ClusterBatchWriter property)

L

label_no_close_muts() (in module seismicrna.core.tests.unbias_test) lateral3 (seismicrna.relate.py.ambindel.Deletion attribute) (seismicrna.relate.py.ambindel.Indel attribute) (seismicrna.relate.py.ambindel.Insertion attribute) lateral5 (seismicrna.relate.py.ambindel.Indel property) length (seismicrna.core.seq.region.Region property) lengthen() (seismicrna.relate.aux.cigarop.CigarOp method) Level (class in seismicrna.core.logs) level (seismicrna.core.logs.Message attribute) level_keys() (seismicrna.core.header.Header class method) level_names() (seismicrna.core.header.Header class method) levels() (seismicrna.core.header.ClustHeader class method) (seismicrna.core.header.Header class method) (seismicrna.core.header.RelHeader class method) line_attrs() (in module seismicrna.relate.sam) linearize_ends_matrix() (in module seismicrna.cluster.jackpot) link_data_dirs_to_tmp() (seismicrna.core.dataset.Dataset method) list() (seismicrna.core.seq.region.RefRegions method) list_actions() (in module seismicrna.tests.wf_test) list_alignments() (in module seismicrna.align.write) list_batch_nums() (in module seismicrna.core.batch.index) list_clusts() (in module seismicrna.core.header) list_fqs_xams() (in module seismicrna.align.write) list_k_clusts() (in module seismicrna.core.header) list_ks_clusts() (in module seismicrna.core.header) list_naturals() (in module seismicrna.core.array) list_pos() (in module seismicrna.lists.listpos) list_profiles() (in module seismicrna.tests.wf_test) list_rels() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 static method) list_step_dir_contents() (in module seismicrna.tests.wf_test) load() (seismicrna.core.io.file.BrickleIO class method) (seismicrna.core.io.file.FileIO class method) (seismicrna.core.report.Report class method) load_abundance_tables() (in module seismicrna.graph.table) load_all_datasets() (in module seismicrna.table) load_brickle() (in module seismicrna.core.io.brickle) load_ct_structs() (in module seismicrna.fold.load)

load_dataset1() (seismicrna.core.dataset.MultistepDataset class method) load_dataset2() (seismicrna.core.dataset.MultistepDataset class method) load_datasets() (in module seismicrna.core.dataset) load_foldable_tables() (in module seismicrna.fold.main) load_function() (seismicrna.cluster.table.ClusterDatasetTabulator class method) (seismicrna.core.table.write.DatasetTabulator class method) (seismicrna.mask.table.MaskDatasetTabulator class method) (seismicrna.relate.table.RelateDatasetTabulator class method) load_input_files() (seismicrna.graph.base.BaseRunner class method) load_param_dir() (in module seismicrna.sim.relate) load_pclust() (in module seismicrna.sim.clusts) load_pends() (in module seismicrna.sim.ends) load_pmut() (in module seismicrna.sim.muts) load_pos_tables() (in module seismicrna.graph.table) load_read_tables() (in module seismicrna.graph.table) load_refseq() (in module seismicrna.relate.tests.main_test) load_regions() (in module seismicrna.mask.main) load_tables() (seismicrna.relate.table.TableLoader class method) LoadedDataset (class in seismicrna.core.dataset) LoadFunction (class in seismicrna.core.dataset) loc_clusters (seismicrna.graph.mutdist.MutationDistanceGraph property) locate() (seismicrna.core.seq.region.RegionFinder static method) locate_elements() (in module seismicrna.core.array) log() (seismicrna.core.logs.Stream method) log_color (seismicrna.core.logs.LoggerConfig attribute) log_command() (in module seismicrna.core.run) log_exceptions() (in module seismicrna.core.logs) log_exp (seismicrna.cluster.em.EMRun property) log_exp_values (seismicrna.cluster.em.EMRun property) log_file_path (seismicrna.core.logs.LoggerConfig attribute) log_like (seismicrna.cluster.em.EMRun property) log_obs (seismicrna.cluster.uniq.UniqReads property) Logger (class in seismicrna.core.logs) LoggerConfig (class in seismicrna.core.logs) loglike_vs_best() (seismicrna.cluster.emk.EMRunsK method) lookup_key() (in module seismicrna.core.report) lookup_title() (in module seismicrna.core.report)

M

make_dict_from_fasta() (in module seismicrna.demult.demultiplex) make_fold_cmd() (in module seismicrna.fold.rnastructure) make_header() (in module seismicrna.core.header) make_path_subject() (in module seismicrna.graph.base) make_pmut_means() (in module seismicrna.sim.muts) make_pmut_means_paired() (in module seismicrna.sim.muts) make_pmut_means_unpaired() (in module seismicrna.sim.muts) make_sequence_objects_from_csv() (in module seismicrna.demult.demultiplex) make_title_action_sample() (in module seismicrna.graph.base) make_tracks() (in module seismicrna.graph.cgroup) makes_dict_from_fastq() (in module seismicrna.demult.demultiplex) map_nested() (in module seismicrna.core.rna.pair) mapq (seismicrna.relate.py.relate.SamRead attribute) marcd_vs_best() (seismicrna.cluster.emk.EMRunsK method) MASK (seismicrna.core.table.base.PositionTable attribute) mask() (seismicrna.mask.write.Masker method) MASK_GU (seismicrna.core.seq.region.Region attribute) mask_gu() (seismicrna.core.seq.region.Region method) MASK_LIST (seismicrna.core.seq.region.Region attribute) mask_list() (seismicrna.core.seq.region.Region method) MASK_NAME (seismicrna.mask.dataset.MaskMutsDataset attribute) mask_names (seismicrna.core.seq.region.Region property) MASK_POLYA (seismicrna.core.seq.region.Region attribute) mask_polya() (seismicrna.core.seq.region.Region method) MASK_POS_FMUT (seismicrna.mask.write.Masker attribute) MASK_POS_NINFO (seismicrna.mask.write.Masker attribute) MASK_READ_DISCONTIG (seismicrna.mask.write.Masker attribute) MASK_READ_FINFO (seismicrna.mask.write.Masker attribute) MASK_READ_FMUT (seismicrna.mask.write.Masker attribute) MASK_READ_GAP (seismicrna.mask.write.Masker attribute) MASK_READ_INIT (seismicrna.mask.write.Masker attribute) MASK_READ_KEPT (seismicrna.mask.write.Masker attribute) MASK_READ_LIST (seismicrna.mask.write.Masker attribute) MASK_READ_NCOV (seismicrna.mask.write.Masker attribute) mask_region() (in module seismicrna.mask.write) mask_segment_ends() (in module seismicrna.core.batch.ends) MaskBatchIO (class in seismicrna.mask.io) MaskBatchTabulator (class in seismicrna.mask.table) MaskCountTabulator (class in seismicrna.mask.table) MaskDataset (class in seismicrna.mask.dataset) MaskDatasetTabulator (class in seismicrna.mask.table) masked_bool (seismicrna.core.seq.region.Region property) masked_int (seismicrna.core.seq.region.Region property) masked_reads_bool (seismicrna.core.batch.read.ReadBatch property) masked_zero (seismicrna.core.seq.region.Region property) Masker (class in seismicrna.mask.write) MaskIO (class in seismicrna.mask.io) MaskMutsBatch (class in seismicrna.mask.batch) MaskMutsDataset (class in seismicrna.mask.dataset) MaskPositionTable (class in seismicrna.mask.table) MaskPositionTableLoader (class in seismicrna.mask.table) MaskPositionTableWriter (class in seismicrna.mask.table) MaskReadBatch (class in seismicrna.mask.batch) MaskReadDataset (class in seismicrna.mask.dataset) MaskReadTable (class in seismicrna.mask.table) MaskReadTableLoader (class in seismicrna.mask.table) MaskReadTableWriter (class in seismicrna.mask.table) MaskReport (class in seismicrna.mask.report) MaskTable (class in seismicrna.mask.table) MaskTabulator (class in seismicrna.mask.table) match_longest_ext() (seismicrna.core.path.Segment method) match_reads_segments() (in module seismicrna.core.batch.ends) matches() (seismicrna.core.rel.pattern.RelPattern class method) matrix (seismicrna.core.batch.muts.RegionMutsBatch property) max_pearson (seismicrna.cluster.em.EMRun property) MAX_PHRED_ENC (seismicrna.align.fqunit.FastqUnit attribute) max_read (seismicrna.core.batch.read.ReadBatch property) (seismicrna.mask.batch.PartialReadBatch property) (seismicrna.relate.batch.FullReadBatch property) max_read_length (seismicrna.graph.mutdist.MutationDistanceGraph property) merge_mates() (in module seismicrna.relate.py.relate) merge_nondemult_fqs() (in module seismicrna.align.write) merge_params() (in module seismicrna.core.arg.cli) merge_read_ends() (in module seismicrna.core.batch.ends) merge_segment_ends() (in module seismicrna.core.batch.ends) MergedDataset (class in seismicrna.core.dataset) MergedRegionDataset (class in seismicrna.core.dataset) MergedUnbiasDataset (class in seismicrna.core.dataset) Message (class in seismicrna.core.logs) migrate_cluster_ref_dir() (in module seismicrna.migrate) migrate_cluster_reg_dir() (in module seismicrna.migrate) migrate_fold_ref_dir() (in module seismicrna.migrate) migrate_fold_reg_dir() (in module seismicrna.migrate) migrate_graph_file() (in module seismicrna.migrate) migrate_graph_ref_dir() (in module seismicrna.migrate) migrate_graph_reg_dir() (in module seismicrna.migrate) migrate_mask_ref_dir() (in module seismicrna.migrate) migrate_mask_reg_dir() (in module seismicrna.migrate) migrate_out_dir() (in module seismicrna.migrate) migrate_relate_ref_dir() (in module seismicrna.migrate) migrate_sample_dir() (in module seismicrna.migrate) migrate_table_ref_dir() (in module seismicrna.migrate) migrate_table_reg_dir() (in module seismicrna.migrate) min_marcd (seismicrna.cluster.em.EMRun property) min_mut_gap (seismicrna.cluster.dataset.ClusterMutsDataset property) (seismicrna.core.dataset.MergedUnbiasDataset property) (seismicrna.core.dataset.UnbiasDataset property) (seismicrna.core.join.JoinMutsDataset property) (seismicrna.mask.dataset.MaskMutsDataset property) (seismicrna.mask.dataset.MaskReadDataset property) MissingBatchError MissingBatchTypeError MissingFastqMate MissingFastqMate1 MissingFastqMate2 MissingFieldWithNoDefaultError MissingReferenceNameError MJOINED (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) mkdir_if_needed() (in module seismicrna.core.path) modified() (seismicrna.core.header.Header method) module seismicrna seismicrna.align seismicrna.align.fqunit seismicrna.align.main seismicrna.align.report seismicrna.align.split seismicrna.align.tests seismicrna.align.tests.write_test seismicrna.align.tests.xamgen_test seismicrna.align.tests.xamops_test seismicrna.align.write seismicrna.align.xamops seismicrna.cleanfa seismicrna.cleanfa.cleanfa seismicrna.cleanfa.main seismicrna.cluster seismicrna.cluster.batch seismicrna.cluster.dataset seismicrna.cluster.em seismicrna.cluster.emk seismicrna.cluster.io seismicrna.cluster.jackpot seismicrna.cluster.main seismicrna.cluster.marginal seismicrna.cluster.names seismicrna.cluster.obsexp seismicrna.cluster.params seismicrna.cluster.report seismicrna.cluster.summary seismicrna.cluster.table seismicrna.cluster.tests seismicrna.cluster.tests.emk_test seismicrna.cluster.tests.jackpot_test seismicrna.cluster.tests.marginal_test seismicrna.cluster.uniq seismicrna.cluster.write seismicrna.core seismicrna.core.arg seismicrna.core.arg.cli seismicrna.core.arg.cmd seismicrna.core.arg.default seismicrna.core.arg.docdef seismicrna.core.array seismicrna.core.batch seismicrna.core.batch.accum seismicrna.core.batch.count seismicrna.core.batch.ends seismicrna.core.batch.index seismicrna.core.batch.muts seismicrna.core.batch.read seismicrna.core.batch.tests seismicrna.core.batch.tests.accum_test seismicrna.core.batch.tests.count_test seismicrna.core.batch.tests.ends_test seismicrna.core.batch.tests.index_test seismicrna.core.batch.tests.muts_test seismicrna.core.dataset seismicrna.core.error seismicrna.core.extern seismicrna.core.extern.depend seismicrna.core.extern.shell seismicrna.core.extern.tests seismicrna.core.header seismicrna.core.io seismicrna.core.io.batch seismicrna.core.io.brickle seismicrna.core.io.file seismicrna.core.io.seq seismicrna.core.io.tests seismicrna.core.io.tests.file_test seismicrna.core.join seismicrna.core.logs seismicrna.core.mu seismicrna.core.mu.compare seismicrna.core.mu.dim seismicrna.core.mu.frame seismicrna.core.mu.measure seismicrna.core.mu.nan seismicrna.core.mu.scale seismicrna.core.mu.tests seismicrna.core.mu.tests.compare_test seismicrna.core.mu.tests.dim_test seismicrna.core.mu.tests.frame_test seismicrna.core.mu.tests.measure_test seismicrna.core.mu.tests.nan_test seismicrna.core.mu.tests.scale_test seismicrna.core.ngs seismicrna.core.ngs.phred seismicrna.core.ngs.tests seismicrna.core.ngs.tests.phred_test seismicrna.core.ngs.tests.xam_test seismicrna.core.ngs.xam seismicrna.core.path seismicrna.core.random seismicrna.core.rel seismicrna.core.rel.code seismicrna.core.rel.pattern seismicrna.core.rel.tests seismicrna.core.rel.tests.code_test seismicrna.core.rel.tests.pattern_test seismicrna.core.report seismicrna.core.rna seismicrna.core.rna.base seismicrna.core.rna.convert seismicrna.core.rna.ct seismicrna.core.rna.db seismicrna.core.rna.io seismicrna.core.rna.pair seismicrna.core.rna.profile seismicrna.core.rna.roc seismicrna.core.rna.state seismicrna.core.rna.struct seismicrna.core.rna.tests seismicrna.core.rna.tests.db_test seismicrna.core.rna.tests.pair_test seismicrna.core.run seismicrna.core.seq seismicrna.core.seq.fasta seismicrna.core.seq.refs seismicrna.core.seq.region seismicrna.core.seq.section seismicrna.core.seq.tests seismicrna.core.seq.tests.fasta_test seismicrna.core.seq.tests.region_test seismicrna.core.seq.tests.xna_test seismicrna.core.seq.xna seismicrna.core.stats seismicrna.core.table seismicrna.core.table.base seismicrna.core.table.write seismicrna.core.task seismicrna.core.tests seismicrna.core.tests.array_test seismicrna.core.tests.header_test seismicrna.core.tests.logs_test seismicrna.core.tests.path_test seismicrna.core.tests.random_test seismicrna.core.tests.stats_test seismicrna.core.tests.task_test seismicrna.core.tests.unbias_test seismicrna.core.tests.version_test seismicrna.core.tmp seismicrna.core.types seismicrna.core.unbias seismicrna.core.version seismicrna.core.write seismicrna.demult seismicrna.demult.demultiplex seismicrna.demult.main seismicrna.draw seismicrna.draw.draw seismicrna.draw.main seismicrna.ensembles seismicrna.export seismicrna.export.main seismicrna.export.meta seismicrna.export.web seismicrna.fold seismicrna.fold.datapath seismicrna.fold.load seismicrna.fold.main seismicrna.fold.report seismicrna.fold.rnastructure seismicrna.graph seismicrna.graph.abundance seismicrna.graph.aucroll seismicrna.graph.base seismicrna.graph.cgroup seismicrna.graph.color seismicrna.graph.corroll seismicrna.graph.dataset seismicrna.graph.delprof seismicrna.graph.giniroll seismicrna.graph.hist seismicrna.graph.histpos seismicrna.graph.histread seismicrna.graph.main seismicrna.graph.mutdist seismicrna.graph.onesource seismicrna.graph.onestruct seismicrna.graph.onetable seismicrna.graph.poscorr seismicrna.graph.pospair seismicrna.graph.profile seismicrna.graph.rel seismicrna.graph.roc seismicrna.graph.roll seismicrna.graph.scatter seismicrna.graph.snrroll seismicrna.graph.statroll seismicrna.graph.table seismicrna.graph.trace seismicrna.graph.twotable seismicrna.join seismicrna.lists seismicrna.lists.listpos seismicrna.lists.lists seismicrna.main seismicrna.mask seismicrna.mask.batch seismicrna.mask.dataset seismicrna.mask.io seismicrna.mask.main seismicrna.mask.report seismicrna.mask.table seismicrna.mask.tests seismicrna.mask.tests.main_test seismicrna.mask.write seismicrna.migrate seismicrna.pool seismicrna.relate seismicrna.relate.aux seismicrna.relate.aux.cigarop seismicrna.relate.aux.infer seismicrna.relate.aux.iterread seismicrna.relate.aux.iterrel seismicrna.relate.aux.tests seismicrna.relate.aux.tests.cigarop_test seismicrna.relate.aux.tests.infer_test seismicrna.relate.aux.tests.iterrel_test seismicrna.relate.batch seismicrna.relate.cx seismicrna.relate.dataset seismicrna.relate.io seismicrna.relate.main seismicrna.relate.py seismicrna.relate.py.ambindel seismicrna.relate.py.cigar seismicrna.relate.py.encode seismicrna.relate.py.error seismicrna.relate.py.relate seismicrna.relate.py.tests seismicrna.relate.py.tests.ambindel_test seismicrna.relate.py.tests.cigar_test seismicrna.relate.py.tests.encode_test seismicrna.relate.report seismicrna.relate.sam seismicrna.relate.sim seismicrna.relate.strands seismicrna.relate.table seismicrna.relate.tests seismicrna.relate.tests.main_test seismicrna.relate.tests.relate_test seismicrna.relate.tests.sam_test seismicrna.relate.write seismicrna.renumct seismicrna.renumct.main seismicrna.sim seismicrna.sim.clusts seismicrna.sim.ends seismicrna.sim.fastq seismicrna.sim.fold seismicrna.sim.main seismicrna.sim.muts seismicrna.sim.params seismicrna.sim.ref seismicrna.sim.relate seismicrna.sim.tests seismicrna.sim.tests.ends_test seismicrna.sim.total seismicrna.table seismicrna.test seismicrna.test.main seismicrna.tests seismicrna.tests.ensembles_test seismicrna.tests.wf_test seismicrna.urls seismicrna.wf

MODULES (seismicrna.tests.ensembles_test.TestEnsembles attribute) move() (seismicrna.relate.py.ambindel.Indel method) MultiRelsGraph (class in seismicrna.graph.rel) MultiRelsProfileGraph (class in seismicrna.graph.profile) MultistepDataset (class in seismicrna.core.dataset) mus (seismicrna.cluster.em.EMRun property) mut_bits (seismicrna.core.rel.pattern.HalfRelPattern attribute) MutationDistanceGraph (class in seismicrna.graph.mutdist) MutationDistanceRunner (class in seismicrna.graph.mutdist) MutationDistanceWriter (class in seismicrna.graph.mutdist) muts (seismicrna.core.batch.muts.MutsBatch property) muts() (seismicrna.core.rel.pattern.HalfRelPattern class method) (seismicrna.core.rel.pattern.RelPattern class method) MutsBatch (class in seismicrna.core.batch.muts) MutsBatchIO (class in seismicrna.core.io.batch) MutsDataset (class in seismicrna.core.dataset)

N

n_reads (seismicrna.align.fqunit.FastqUnit property) (seismicrna.cluster.em.EMRun property) (seismicrna.relate.sam.XamViewer property) n_reads_discontig (seismicrna.mask.write.Masker property) n_reads_init (seismicrna.mask.write.Masker property) n_reads_kept (seismicrna.mask.write.Masker property) n_reads_list (seismicrna.mask.write.Masker property) n_reads_max_fmut (seismicrna.mask.write.Masker property) n_reads_min_finfo (seismicrna.mask.write.Masker property) n_reads_min_gap (seismicrna.mask.write.Masker property) n_reads_min_ncov (seismicrna.mask.write.Masker property) n_runs_passing() (seismicrna.cluster.emk.EMRunsK method) name (seismicrna.core.task.Task property) (seismicrna.relate.py.relate.SamRead attribute) name_batch_attrs() (seismicrna.cluster.dataset.JoinClusterMutsDataset class method) (seismicrna.core.join.JoinMutsDataset class method) (seismicrna.mask.dataset.JoinMaskMutsDataset class method) names (seismicrna.core.header.Header property) NamesDataset (class in seismicrna.relate.dataset) ncols (seismicrna.graph.cgroup.ClusterGroupGraph property) need_write() (in module seismicrna.core.write) no_close_muts() (in module seismicrna.core.tests.unbias_test) no_nan() (in module seismicrna.core.mu.nan) none() (seismicrna.core.rel.pattern.HalfRelPattern class method) normalize() (in module seismicrna.core.mu.scale)

nos (seismicrna.core.rel.pattern.RelPattern attribute) nrows (seismicrna.graph.cgroup.ClusterGroupGraph property) num_batches (seismicrna.cluster.uniq.UniqReads property) (seismicrna.core.dataset.Dataset property) (seismicrna.core.dataset.LoadedDataset property) (seismicrna.core.dataset.MultistepDataset property) (seismicrna.core.dataset.TallDataset property) (seismicrna.core.dataset.WideDataset property) num_contiguous (seismicrna.core.batch.ends.EndCoords property) num_discontiguous (seismicrna.core.batch.ends.EndCoords property) num_levels() (seismicrna.core.header.Header class method) num_nonuniq (seismicrna.cluster.uniq.UniqReads property) num_obs (seismicrna.cluster.uniq.UniqReads property) num_reads (seismicrna.cluster.batch.ClusterReadBatch property) (seismicrna.core.batch.ends.EndCoords property) (seismicrna.core.batch.read.ReadBatch property) (seismicrna.core.dataset.Dataset property) (seismicrna.core.table.write.Tabulator property) (seismicrna.mask.batch.MaskReadBatch property) (seismicrna.relate.batch.ReadNamesBatch property) (seismicrna.relate.write.RelationWriter property) num_segments (seismicrna.core.batch.ends.EndCoords property) num_uniq (seismicrna.cluster.uniq.UniqReads property) NUMBERS (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) nums_batches (seismicrna.core.dataset.TallDataset property)

O

oconv (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) oconv_datetime() (in module seismicrna.core.report) OneRelGraph (class in seismicrna.graph.rel) OneRelProfileGraph (class in seismicrna.graph.profile) OneSourceClusterGroupGraph (class in seismicrna.graph.onesource) OneSourceGraph (class in seismicrna.graph.onesource) OneTableGraph (class in seismicrna.graph.onetable) OneTableRelClusterGroupGraph (class in seismicrna.graph.onetable) OneTableRelClusterGroupRunner (class in seismicrna.graph.onetable) OneTableRelClusterGroupWriter (class in seismicrna.graph.onetable) OneTableRunner (class in seismicrna.graph.onetable) OneTableWriter (class in seismicrna.graph.onetable) op (seismicrna.relate.aux.cigarop.CigarOp property)

op_consumes_read() (in module seismicrna.relate.py.cigar) op_consumes_ref() (in module seismicrna.relate.py.cigar) op_is_mutation() (in module seismicrna.relate.aux.cigarop) open_url() (in module seismicrna.urls) opposite (seismicrna.relate.py.ambindel.Deletion attribute) (seismicrna.relate.py.ambindel.Indel attribute) (seismicrna.relate.py.ambindel.Insertion attribute) ops (seismicrna.relate.aux.tests.cigarop_test.TestCigarOp attribute) optional_path() (in module seismicrna.core.arg.cli) OptionField (class in seismicrna.core.report) OUT_DIR (seismicrna.tests.wf_test.TestWorkflow attribute) (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) OUT_DIRS (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) OutOfBoundsError

P

p_ends_given_clust_noclose (seismicrna.mask.table.PartialTabulator property) paired (seismicrna.relate.dataset.RelateMutsDataset property) (seismicrna.relate.py.relate.SamFlag attribute) (seismicrna.relate.sam.XamViewer property) pairs (seismicrna.core.rna.struct.RNAStructure property) pairs_to_dict() (in module seismicrna.core.rna.pair) pairs_to_table() (in module seismicrna.core.rna.pair) parallel_grepping() (in module seismicrna.demult.demultiplex) param_defaults() (in module seismicrna.core.arg.docdef) param_docstrs() (in module seismicrna.core.arg.docdef) params() (seismicrna.graph.base.BaseRunner class method) parent (seismicrna.align.fqunit.FastqUnit property) parse() (in module seismicrna.core.path) (seismicrna.core.path.Field method) (seismicrna.core.path.Path method) (seismicrna.core.path.Segment method) parse_all_scores() (seismicrna.align.tests.xamgen_test.TestAlignmentScoreParams method) parse_bowtie2() (in module seismicrna.align.xamops) parse_cigar() (in module seismicrna.relate.py.cigar) parse_color_file() (in module seismicrna.draw.draw) parse_ct() (in module seismicrna.core.rna.ct) parse_db() (in module seismicrna.core.rna.db) parse_db_strings() (in module seismicrna.core.rna.db) parse_db_structure() (in module seismicrna.core.rna.db) parse_energy() (in module seismicrna.fold.rnastructure) parse_fasta() (in module seismicrna.core.seq.fasta) parse_flagstat() (in module seismicrna.core.ngs.xam) parse_header() (in module seismicrna.core.header) parse_idxstats() (in module seismicrna.core.ngs.xam) parse_join_clusts_file() (in module seismicrna.join) parse_path() (seismicrna.core.io.file.FileIO class method) parse_ref_header() (in module seismicrna.core.ngs.xam) parse_refs_metadata() (in module seismicrna.export.meta) parse_rnastructure_ct_title() (in module seismicrna.fold.rnastructure) parse_samples_metadata() (in module seismicrna.export.meta) parse_scores() (seismicrna.align.tests.xamgen_test.TestAlignmentScoreParams static method) parse_stdout_count_fastq_reads() (in module seismicrna.align.fqunit) parse_top_separate() (in module seismicrna.core.path) parse_version() (in module seismicrna.core.version) PartialDatasetTabulator (class in seismicrna.mask.table) PartialPositionTable (class in seismicrna.mask.table) PartialReadBatch (class in seismicrna.mask.batch) PartialReadTable (class in seismicrna.mask.table) PartialRegionMutsBatch (class in seismicrna.mask.batch) PartialTable (class in seismicrna.mask.table) PartialTabulator (class in seismicrna.mask.table) passing() (seismicrna.cluster.emk.EMRunsK method) Path (class in seismicrna.core.path) path (seismicrna.core.table.base.Table property) path_field_values() (seismicrna.core.io.file.FileIO method) path_fields (seismicrna.core.table.base.Table property) (seismicrna.mask.table.PartialTable property) (seismicrna.relate.table.FullTable property) path_fields() (seismicrna.core.io.file.FileIO class method) path_matches() (in module seismicrna.core.path) path_segs() (seismicrna.core.table.base.AbundanceTable class method) (seismicrna.core.table.base.Table class method) (seismicrna.mask.table.PartialPositionTable class method) (seismicrna.mask.table.PartialReadTable class method) (seismicrna.relate.report.PoolReport class method) (seismicrna.relate.table.FullPositionTable class method) (seismicrna.relate.table.FullReadTable class method) path_subject (seismicrna.graph.abundance.ClusterAbundanceGraph property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.graph.onesource.OneSourceClusterGroupGraph property) (seismicrna.graph.onestruct.StructOneTableGraph property) (seismicrna.graph.twotable.TwoTableRelClusterGroupGraph property) path_subject1 (seismicrna.graph.twotable.TwoTableRelClusterGroupGraph property) path_subject2 (seismicrna.graph.twotable.TwoTableRelClusterGroupGraph property) PathError PathTypeError

PathValueError pattern (seismicrna.cluster.dataset.ClusterMutsDataset property) (seismicrna.cluster.dataset.ClusterReadDataset property) (seismicrna.core.dataset.Dataset property) (seismicrna.core.dataset.MergedDataset property) (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.mask.dataset.MaskMutsDataset property) (seismicrna.mask.dataset.MaskReadDataset property) (seismicrna.relate.dataset.ReadNamesDataset property) (seismicrna.relate.dataset.RelateMutsDataset property) PATTERN_KEY (seismicrna.mask.write.Masker attribute) patterns (seismicrna.core.rel.pattern.HalfRelPattern property) pearson_vs_best() (seismicrna.cluster.emk.EMRunsK method) phred_arg (seismicrna.align.fqunit.FastqUnit property) pict() (seismicrna.core.seq.xna.DNA class method) (seismicrna.core.seq.xna.RNA class method) (seismicrna.core.seq.xna.XNA class method) picto (seismicrna.core.seq.xna.XNA property) pis (seismicrna.cluster.em.EMRun property) pod (seismicrna.relate.py.ambindel.Deletion attribute) (seismicrna.relate.py.ambindel.Indel attribute) (seismicrna.relate.py.ambindel.Insertion attribute) pool_samples() (in module seismicrna.pool) PoolDataset (class in seismicrna.relate.dataset) POOLED (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) PoolReadNamesDataset (class in seismicrna.relate.dataset) PoolReport (class in seismicrna.relate.report) pos (seismicrna.relate.py.relate.SamRead attribute) pos3 (seismicrna.core.seq.region.RegionTuple attribute) pos5 (seismicrna.core.seq.region.RegionTuple attribute) pos_dtype (seismicrna.core.batch.ends.EndCoords property) pos_gu (seismicrna.mask.write.Masker property) pos_header (seismicrna.core.table.write.Tabulator property) pos_index (seismicrna.core.batch.muts.RegionMutsBatch property) pos_kept (seismicrna.mask.dataset.MaskReadDataset property) (seismicrna.mask.write.Masker property) pos_list (seismicrna.mask.write.Masker property) pos_max_fmut (seismicrna.mask.write.Masker property) pos_min_ninfo (seismicrna.mask.write.Masker property) pos_nums (seismicrna.core.batch.muts.MutsBatch property) pos_polya (seismicrna.mask.write.Masker property) PositionCorrelationGraph (class in seismicrna.graph.poscorr) PositionCorrelationRunner (class in seismicrna.graph.poscorr) PositionCorrelationWriter (class in seismicrna.graph.poscorr) PositionHistogramGraph (class in seismicrna.graph.histpos) PositionHistogramRunner (class in seismicrna.graph.histpos) PositionHistogramWriter (class in seismicrna.graph.histpos) PositionPairGraph (class in seismicrna.graph.pospair) PositionPairRunner (class in seismicrna.graph.pospair) PositionPairWriter (class in seismicrna.graph.pospair) PositionTable (class in seismicrna.core.table.base) PositionTableLoader (class in seismicrna.relate.table) PositionTableRunner (class in seismicrna.graph.table) PositionTableWriter (class in seismicrna.core.table.write) powerset() (in module seismicrna.core.rel.tests.pattern_test) predicate (seismicrna.graph.abundance.ClusterAbundanceGraph property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.corroll.RollingCorrelationGraph property) (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.graph.roll.RollingGraph property) (seismicrna.graph.table.RelTableGraph property) process_struct() (seismicrna.draw.draw.RNArtistRun method) profile (seismicrna.core.rna.profile.RNAProfile property) PROFILE (seismicrna.tests.ensembles_test.TestEnsembles attribute) profile_names (seismicrna.graph.aucroll.RollingAUCGraph property) (seismicrna.graph.roc.ROCGraph property) ProfileGraph (class in seismicrna.graph.profile) ProfileRunner (class in seismicrna.graph.profile) ProfileWriter (class in seismicrna.graph.profile) proper (seismicrna.relate.py.relate.SamFlag attribute) proportions (seismicrna.core.table.base.AbundanceTable property) ptrn_fancy (seismicrna.core.rel.pattern.HalfRelPattern attribute) ptrn_plain (seismicrna.core.rel.pattern.HalfRelPattern attribute)

Q

quals (seismicrna.relate.py.relate.SamRead attribute) quick_unbias (seismicrna.cluster.dataset.ClusterMutsDataset property) (seismicrna.core.dataset.MergedUnbiasDataset property) (seismicrna.core.dataset.UnbiasDataset property) (seismicrna.mask.dataset.MaskMutsDataset property) (seismicrna.mask.dataset.MaskReadDataset property)

quick_unbias_thresh (seismicrna.cluster.dataset.ClusterMutsDataset property) (seismicrna.core.dataset.MergedUnbiasDataset property) (seismicrna.core.dataset.UnbiasDataset property) (seismicrna.mask.dataset.MaskMutsDataset property) (seismicrna.mask.dataset.MaskReadDataset property)

R

raise_on_error (seismicrna.core.logs.Logger attribute) (seismicrna.core.logs.LoggerConfig attribute) rand_dirichlet_alpha() (in module seismicrna.core.tests.stats_test) randdir() (in module seismicrna.core.path) random() (seismicrna.core.seq.xna.XNA class method) random_params() (seismicrna.core.tests.unbias_test.TestQuickUnbias static method) range (seismicrna.core.seq.region.Region property) (seismicrna.core.table.base.PositionTable property) range_int (seismicrna.core.seq.region.Region property) (seismicrna.core.table.base.PositionTable property) range_one (seismicrna.core.seq.region.Region property) rc (seismicrna.core.seq.xna.XNA property) read1 (seismicrna.relate.py.relate.SamFlag attribute) read2 (seismicrna.relate.py.relate.SamFlag attribute) read_bases (seismicrna.core.rel.pattern.HalfRelPattern attribute) read_dtype (seismicrna.core.batch.read.ReadBatch property) read_end3s (seismicrna.core.batch.ends.EndCoords property) read_end3s_zero (seismicrna.cluster.uniq.UniqReads property) read_end5s (seismicrna.core.batch.ends.EndCoords property) read_end5s_zero (seismicrna.cluster.uniq.UniqReads property) read_end_counts (seismicrna.core.batch.muts.MutsBatch property) read_header (seismicrna.core.table.write.Tabulator property) read_indexes (seismicrna.core.batch.read.ReadBatch property) (seismicrna.mask.batch.PartialReadBatch property) (seismicrna.relate.batch.FullReadBatch property) read_lengths (seismicrna.core.batch.ends.EndCoords property) read_names_dataset (seismicrna.mask.write.Masker property) read_nums (seismicrna.cluster.batch.ClusterReadBatch property) (seismicrna.core.batch.read.ReadBatch property) (seismicrna.mask.batch.MaskReadBatch property) (seismicrna.relate.batch.FullReadBatch property) read_weights (seismicrna.cluster.batch.ClusterMutsBatch property) (seismicrna.core.batch.muts.MutsBatch property) (seismicrna.mask.batch.MaskMutsBatch property) (seismicrna.relate.batch.RelateBatch property) ReadBatch (class in seismicrna.core.batch.read) ReadBatchIO (class in seismicrna.core.io.batch) ReadHistogramGraph (class in seismicrna.graph.histread) ReadHistogramRunner (class in seismicrna.graph.histread) ReadHistogramWriter (class in seismicrna.graph.histread) ReadNamesBatch (class in seismicrna.relate.batch) ReadNamesBatchIO (class in seismicrna.relate.io) ReadNamesDataset (class in seismicrna.relate.dataset) reads (seismicrna.core.table.base.ReadTable property) reads_noclose_muts() (seismicrna.core.batch.muts.RegionMutsBatch method) reads_per_batch() (seismicrna.mask.tests.main_test.TestMask class method) (seismicrna.mask.tests.main_test.TestMask1Batch class method) (seismicrna.mask.tests.main_test.TestMaskBatches class method) reads_per_pos() (seismicrna.core.batch.muts.RegionMutsBatch method) reads_per_sample() (seismicrna.mask.tests.main_test.TestMask class method) (seismicrna.mask.tests.main_test.TestMask1Sample class method) (seismicrna.mask.tests.main_test.TestMask2Samples class method) ReadTable (class in seismicrna.core.table.base) ReadTableLoader (class in seismicrna.relate.table) ReadTableRunner (class in seismicrna.graph.table) ReadTableWriter (class in seismicrna.core.table.write) realign_cmd() (in module seismicrna.align.xamops) recast_file_path() (in module seismicrna.core.io.file) REF (seismicrna.cluster.tests.jackpot_test.TestBootstrapJackpotScores attribute) ref (seismicrna.cluster.uniq.UniqReads property) (seismicrna.core.dataset.Dataset property) (seismicrna.core.rna.base.RNARegion property) (seismicrna.core.table.base.Table property) (seismicrna.core.table.write.TableWriter property) (seismicrna.core.table.write.Tabulator property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) (seismicrna.relate.py.relate.SamRead attribute) (seismicrna.relate.sam.XamViewer property) (seismicrna.relate.table.TableLoader property) (seismicrna.relate.write.RelationWriter property) REF (seismicrna.tests.ensembles_test.TestEnsembles attribute) (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) ref_bases (seismicrna.core.rel.pattern.HalfRelPattern attribute) ref_header_cmd() (in module seismicrna.core.ngs.xam) ref_reg (seismicrna.core.seq.region.Region property) ref_to_alignments() (in module seismicrna.relate.aux.iterread) ReferenceNameError RefIO (class in seismicrna.core.io.file) reflen (seismicrna.core.dataset.RegionDataset property) reframe() (in module seismicrna.core.mu.frame) reframe_like() (in module seismicrna.core.mu.frame) RefRegions (class in seismicrna.core.seq.region) REFS (seismicrna.cluster.tests.jackpot_test.TestBootstrapJackpotScores attribute) refs (seismicrna.core.seq.region.RefRegions property) REFS (seismicrna.tests.ensembles_test.TestEnsembles attribute) (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) refs() (seismicrna.core.rel.pattern.HalfRelPattern class method) refseq (seismicrna.core.dataset.MergedRegionDataset property) (seismicrna.core.dataset.MultistepDataset property) (seismicrna.core.dataset.RegionDataset property) (seismicrna.core.io.seq.RefseqIO property) (seismicrna.core.table.base.Table property) (seismicrna.core.table.write.TableWriter property) (seismicrna.relate.dataset.RelateMutsDataset property) (seismicrna.relate.table.TableLoader property) refseq_file() (seismicrna.relate.report.RelateReport method) refseq_file_auto_fields() (in module seismicrna.relate.report) refseq_file_path() (in module seismicrna.relate.report) refseq_file_seg_types() (in module seismicrna.relate.report) RefseqIO (class in seismicrna.core.io.seq) RefseqReport (class in seismicrna.core.report) RefSeqs (class in seismicrna.core.seq.refs) reg (seismicrna.core.rna.base.RNARegion property) (seismicrna.core.table.base.Table property) (seismicrna.core.table.write.TableWriter property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) (seismicrna.relate.table.TableLoader property) RegIO (class in seismicrna.core.io.file) Region (class in seismicrna.core.seq.region) region (seismicrna.cluster.dataset.ClusterMutsDataset property) (seismicrna.core.dataset.RegionDataset property) (seismicrna.core.dataset.WideDataset property) (seismicrna.core.rna.struct.Rna2dStemLoop property) (seismicrna.core.table.base.PositionTable property) (seismicrna.mask.dataset.MaskMutsDataset property) (seismicrna.relate.dataset.PoolDataset property) (seismicrna.relate.dataset.RelateMutsDataset property) region3 (seismicrna.core.rna.struct.Rna2dStem property) region5 (seismicrna.core.rna.struct.Rna2dStem property) region_end5 (seismicrna.cluster.em.EMRun property) region_names (seismicrna.core.dataset.WideDataset property) RegionDataset (class in seismicrna.core.dataset) RegionFinder (class in seismicrna.core.seq.region) RegionInfo (class in seismicrna.ensembles) RegionMutsBatch (class in seismicrna.core.batch.muts) regions (seismicrna.core.seq.region.RefRegions property) RegionTuple (class in seismicrna.core.seq.region) regular_grepping() (in module seismicrna.demult.demultiplex) rel_name (seismicrna.graph.rel.OneRelGraph property) rel_names (seismicrna.graph.rel.MultiRelsGraph property) (seismicrna.graph.rel.OneRelGraph property) (seismicrna.graph.rel.RelGraph property) REL_TOL (seismicrna.core.tests.unbias_test.TestQuickUnbias attribute) relate() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) relate_error() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) relate_records() (in module seismicrna.relate.write) relate_truncated() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) relate_xam() (in module seismicrna.relate.write) RelateBatch (class in seismicrna.relate.batch) RelateBatchIO (class in seismicrna.relate.io) RelateBatchTabulator (class in seismicrna.relate.table) RelateCountTabulator (class in seismicrna.relate.table) RelateDataset (class in seismicrna.relate.dataset) RelateDatasetTabulator (class in seismicrna.relate.table) RelateError RelateIO (class in seismicrna.relate.io) RelateMutsDataset (class in seismicrna.relate.dataset) RelatePositionTable (class in seismicrna.relate.table) RelatePositionTableLoader (class in seismicrna.relate.table) RelatePositionTableWriter (class in seismicrna.relate.table)

RelateReadTable (class in seismicrna.relate.table) RelateReadTableLoader (class in seismicrna.relate.table) RelateReadTableWriter (class in seismicrna.relate.table) RelateReport (class in seismicrna.relate.report) RelateTable (class in seismicrna.relate.table) RelateTabulator (class in seismicrna.relate.table) relationships (seismicrna.graph.rel.RelGraph property) RelationWriter (class in seismicrna.relate.write) RelClustHeader (class in seismicrna.core.header) RelColorMap (class in seismicrna.graph.color) release_to_out() (in module seismicrna.core.tmp) RelGraph (class in seismicrna.graph.rel) RelHeader (class in seismicrna.core.header) RelPattern (class in seismicrna.core.rel.pattern) RelRunner (class in seismicrna.graph.rel) rels (seismicrna.core.header.RelHeader property) rels_per_pos (seismicrna.core.batch.muts.RegionMutsBatch property) rels_per_read (seismicrna.core.batch.muts.RegionMutsBatch property) RelTableGraph (class in seismicrna.graph.table) RelTableRunner (class in seismicrna.graph.table) RelTypeTable (class in seismicrna.core.table.base) RelTypeTableLoader (class in seismicrna.relate.table) remove_mask() (seismicrna.core.seq.region.Region method) remove_nan() (in module seismicrna.core.mu.nan) removes_nan() (in module seismicrna.core.mu.nan) rename_columns() (in module seismicrna.graph.roc) renumber_ct() (in module seismicrna.core.rna.io) renumber_from() (seismicrna.core.rna.base.RNARegion method) (seismicrna.core.seq.region.Region method) renumber_pairs() (in module seismicrna.core.rna.pair) Report (class in seismicrna.core.report) report_path_auto_fields (seismicrna.core.dataset.LoadFunction property) report_path_seg_types (seismicrna.core.dataset.LoadFunction property) ReportDoesNotHaveFieldError ReportFieldAttributeError ReportFieldError ReportFieldKeyError ReportFieldTypeError ReportFieldValueError require_data_path() (in module seismicrna.fold.rnastructure) require_dependency() (in module seismicrna.core.extern.depend) require_env_var() (in module seismicrna.core.extern.depend) resample() (seismicrna.core.table.base.PositionTable method) RESET (seismicrna.core.logs.AnsiCode attribute) reset() (seismicrna.core.logs.AnsiCode class method) resolve_or_analyze_multigrepped_reads() (in module seismicrna.demult.demultiplex) restore_config() (in module seismicrna.core.logs) retitle_ct() (in module seismicrna.fold.rnastructure) rev (seismicrna.relate.py.relate.SamFlag attribute) reverse_compliment() (in module seismicrna.demult.demultiplex) ReversedTimeStampError rmdir_if_needed() (in module seismicrna.core.path) RNA (class in seismicrna.core.seq.xna) Rna2dPart (class in seismicrna.core.rna.struct) Rna2dStem (class in seismicrna.core.rna.struct) Rna2dStemLoop (class in seismicrna.core.rna.struct) RnaJunction (class in seismicrna.core.rna.struct) RNAProfile (class in seismicrna.core.rna.profile) RNARegion (class in seismicrna.core.rna.base) RNArtistRun (class in seismicrna.draw.draw) RNAState (class in seismicrna.core.rna.state) RNAStructure (class in seismicrna.core.rna.struct) RNAStructureConnectivityTableTitleLineFormatError roc (seismicrna.core.rna.state.RNAState property) ROCGraph (class in seismicrna.graph.roc) ROCRunner (class in seismicrna.graph.roc) ROCWriter (class in seismicrna.graph.roc) rolling_auc() (seismicrna.core.rna.state.RNAState method) RollingAUCGraph (class in seismicrna.graph.aucroll) RollingAUCRunner (class in seismicrna.graph.aucroll) RollingAUCWriter (class in seismicrna.graph.aucroll) RollingCorrelationGraph (class in seismicrna.graph.corroll) RollingCorrelationRunner (class in seismicrna.graph.corroll) RollingCorrelationWriter (class in seismicrna.graph.corroll) RollingGiniGraph (class in seismicrna.graph.giniroll) RollingGiniRunner (class in seismicrna.graph.giniroll) RollingGiniWriter (class in seismicrna.graph.giniroll) RollingGraph (class in seismicrna.graph.roll) RollingRunner (class in seismicrna.graph.roll) RollingSNRGraph (class in seismicrna.graph.snrroll) RollingSNRRunner (class in seismicrna.graph.snrroll) RollingSNRWriter (class in seismicrna.graph.snrroll) RollingStatGraph (class in seismicrna.graph.statroll) RollingStatRunner (class in seismicrna.graph.statroll) RollingStatWriter (class in seismicrna.graph.statroll) roots (seismicrna.core.rna.struct.RNAStructure property) ROUTINE (seismicrna.core.logs.Level attribute) routine() (seismicrna.core.logs.Logger method) row_titles (seismicrna.graph.cgroup.ClusterGroupGraph property) row_tracks (seismicrna.graph.abundance.ClusterAbundanceGraph property) (seismicrna.graph.cgroup.ClusterGroupGraph property) (seismicrna.graph.mutdist.MutationDistanceGraph property) (seismicrna.graph.onetable.OneTableRelClusterGroupGraph property) (seismicrna.graph.pospair.PositionPairGraph property) (seismicrna.graph.twotable.TwoTableRelClusterGroupGraph property) rt() (seismicrna.core.seq.xna.RNA method) run() (in module seismicrna.align.main) (in module seismicrna.align.split) (in module seismicrna.cleanfa.main) (in module seismicrna.cluster.main) (in module seismicrna.draw.main) (in module seismicrna.ensembles) (in module seismicrna.export.main) (in module seismicrna.fold.main) (in module seismicrna.join) (in module seismicrna.lists.listpos) (in module seismicrna.mask.main) (in module seismicrna.migrate) (in module seismicrna.pool) (in module seismicrna.relate.main) (in module seismicrna.renumct.main) (in module seismicrna.sim.clusts) (in module seismicrna.sim.ends) (in module seismicrna.sim.fastq) (in module seismicrna.sim.fold) (in module seismicrna.sim.muts) (in module seismicrna.sim.params) (in module seismicrna.sim.ref) (in module seismicrna.sim.relate) (in module seismicrna.sim.total) (in module seismicrna.table) (in module seismicrna.test.main) (in module seismicrna.wf) (seismicrna.cleanfa.cleanfa.FastaCleaner method) (seismicrna.draw.draw.RNArtistRun method) (seismicrna.graph.abundance.ClusterAbundanceRunner class method) (seismicrna.graph.aucroll.RollingAUCRunner class method) (seismicrna.graph.base.BaseRunner class method) (seismicrna.graph.corroll.RollingCorrelationRunner class method) (seismicrna.graph.dataset.DatasetRunner class method) (seismicrna.graph.delprof.DeltaProfileRunner class method) (seismicrna.graph.giniroll.RollingGiniRunner class method) (seismicrna.graph.histpos.PositionHistogramRunner class method) (seismicrna.graph.histread.ReadHistogramRunner class method) (seismicrna.graph.mutdist.MutationDistanceRunner class method) (seismicrna.graph.onetable.OneTableRunner class method) (seismicrna.graph.poscorr.PositionCorrelationRunner class method) (seismicrna.graph.profile.ProfileRunner class method) (seismicrna.graph.roc.ROCRunner class method) (seismicrna.graph.scatter.ScatterRunner class method) (seismicrna.graph.snrroll.RollingSNRRunner class method) (seismicrna.graph.twotable.TwoTableRunner class method) run_cmd() (in module seismicrna.core.extern.shell) run_ct_to_db() (in module seismicrna.core.rna.convert) run_datapath() (in module seismicrna.fold.datapath) run_db_to_ct() (in module seismicrna.core.rna.convert) run_dm() (in module seismicrna.demult.main) run_ensembles() (seismicrna.tests.ensembles_test.TestEnsembles method) run_func() (in module seismicrna.core.run) run_k() (in module seismicrna.cluster.write) run_ks() (in module seismicrna.cluster.write) run_multi_greps() (in module seismicrna.demult.demultiplex) run_passing() (seismicrna.cluster.emk.EMRunsK method) run_seqkit_grep() (in module seismicrna.demult.demultiplex) run_seqkit_grep_function() (in module seismicrna.demult.demultiplex) run_struct() (in module seismicrna.sim.muts) run_test_invalid() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) run_test_valid() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method)

S

SamFlag (class in seismicrna.relate.py.relate) SAMPLE (seismicrna.cluster.tests.jackpot_test.TestBootstrapJackpotScores attribute) sample (seismicrna.core.dataset.Dataset property) (seismicrna.core.table.base.Table property) (seismicrna.core.table.write.TableWriter property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) (seismicrna.relate.sam.XamViewer property) (seismicrna.relate.table.TableLoader property) (seismicrna.relate.write.RelationWriter property) SAMPLE (seismicrna.tests.ensembles_test.TestEnsembles attribute) (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) sample1 (seismicrna.graph.twotable.TwoTableGraph property) sample2 (seismicrna.graph.twotable.TwoTableGraph property) samples (seismicrna.core.dataset.TallDataset property) SamRead (class in seismicrna.relate.py.relate) sanitize() (in module seismicrna.core.path) sanitize_muts() (in module seismicrna.core.batch.muts) sanitize_segment_ends() (in module seismicrna.core.batch.ends) sanitize_values() (in module seismicrna.core.array) save() (seismicrna.core.io.file.BrickleIO method) (seismicrna.core.io.file.FileIO method) (seismicrna.core.report.Report method) save_brickle() (in module seismicrna.core.io.brickle) ScatterGraph (class in seismicrna.graph.scatter) ScatterRunner (class in seismicrna.graph.scatter) ScatterWriter (class in seismicrna.graph.scatter) seg_end3s (seismicrna.core.batch.ends.EndCoords property) seg_end3s_zero (seismicrna.cluster.uniq.UniqReads property) seg_end5s (seismicrna.core.batch.ends.EndCoords property) seg_end5s_zero (seismicrna.cluster.uniq.UniqReads property) seg_types (seismicrna.align.fqunit.FastqUnit property) seg_types() (seismicrna.core.io.file.FileIO class method) Segment (class in seismicrna.core.path) seismic-align command line option --bt2-contain --bt2-D --bt2-discordant --bt2-dovetail --bt2-dpad --bt2-end-to-end --bt2-gbar --bt2-I --bt2-i --bt2-L --bt2-local --bt2-mixed --bt2-no-contain --bt2-no-discordant --bt2-no-dovetail --bt2-no-mixed --bt2-no-un --bt2-orient --bt2-R --bt2-score-min-e2e --bt2-score-min-loc --bt2-un --bt2-X --dmfastqx --dmfastqy --dmfastqz --erase-tmp --f1r2-fwd --f1r2-rev --fastp --fastp-3 --fastp-5 --fastp-adapter-1 --fastp-adapter-2 --fastp-adapter-fasta --fastp-adapter-trimming --fastp-detect-adapter-for-pe --fastp-m --fastp-min-length --fastp-poly-g --fastp-poly-g-min-len --fastp-poly-x --fastp-poly-x-min-len --fastp-w --fastqx --fastqy --fastqz --force --keep-tmp --max-procs --min-mapq --min-reads --mix-strands --no-fastp --no-fastp-3 --no-fastp-5 --no-fastp-adapter-trimming --no-fastp-detect-adapter-for-pe --no-fastp-poly-x --no-force --out-dir --phred-enc --rev-label --sep-strands --tmp-pfx -N -o -t -x -X -y -Y -z -Z FASTA seismic-cleanfa command line option --force --inplace --max-procs --no-force --no-inplace --out-dir -o INPUT_PATH seismic-cluster command line option --brotli-level --cluster-abundance-table --cluster-pos-table --em-runs --em-thresh --erase-tmp --force --jackpot --jackpot-conf-level --keep-tmp --max-clusters --max-em-iter --max-jackpot-quotient --max-loglike-vs-best --max-marcd-vs-best --max-pearson-run --max-procs --min-clusters --min-em-iter --min-marcd-run --min-pearson-vs-best --no-cluster-abundance-table --no-cluster-pos-table --no-force --no-jackpot --no-verify-times --stop-best-k --tmp-pfx --try-all-ks --verify-times --write-all-ks --write-best-k -e -k -t INPUT_PATH seismic-demult command line option --barcode-end --barcode-start --clipped --demulti-overwrite --erase-tmp --fastqx --index-tolerance --keep-tmp --mismatch-tolerence --out-dir --parallel-demultiplexing --phred-enc --refs-meta --tmp-pfx -o -R -t -x FASTA seismic-fold command line option --erase-tmp --fold-constraint --fold-coords --fold-full --fold-max --fold-md --fold-mfe --fold-percent --fold-primers --fold-regions-file --fold-sub --fold-table --fold-temp --force --keep-tmp --max-procs --no-force --quantile --tmp-pfx -f -q -t INPUT_PATH seismic-graph-aucroll command line option --cgroup --csv --fold-coords --fold-full --fold-primers --fold-regions-file --fold-table --force --html --max-procs --no-csv --no-force --no-html --no-pdf --no-png --no-svg --pdf --png --quantile --rels --struct-file --svg --use-count --use-ratio --window --winmin -f -n -q -r -w INPUT_PATH seismic-graph-corroll command line option --cgroup --comppair --compself --csv --force --html --max-procs --metric --no-comppair --no-compself --no-csv --no-force --no-html --no-pdf --no-png --no-svg --out-dir --pdf --png --quantile --rels --svg --use-count --use-ratio --window --winmin -m -n -o -q -r -w INPUT_PATH seismic-graph-delprof command line option --cgroup --comppair --compself --csv --force --html --max-procs --no-comppair --no-compself --no-csv --no-force --no-html --no-pdf --no-png --no-svg --out-dir --pdf --png --quantile --rels --svg --use-count --use-ratio -o -q -r INPUT_PATH seismic-graph-histpos command line option --cgroup --csv --force --hist-bins --hist-margin --html --max-procs --no-csv --no-force --no-html --no-pdf --no-png --no-svg --pdf --png --quantile --rels --svg --use-count --use-ratio -q -r INPUT_PATH seismic-graph-histread command line option --cgroup --csv --force --hist-bins --hist-margin --html --max-procs --no-csv --no-force --no-html --no-pdf --no-png --no-svg --pdf --png --quantile --rels --svg --use-count --use-ratio -q -r INPUT_PATH seismic-graph-profile command line option --cgroup --csv --force --html --max-procs --no-csv --no-force --no-html --no-pdf --no-png --no-svg --pdf --png --quantile --rels --svg --use-count --use-ratio -q -r INPUT_PATH seismic-graph-roc command line option --cgroup --csv --fold-coords --fold-full --fold-primers --fold-regions-file --fold-table --force --html --max-procs --no-csv --no-force --no-html --no-pdf --no-png --no-svg --pdf --png --quantile --rels --struct-file --svg --use-count --use-ratio -f -q -r INPUT_PATH seismic-graph-scatter command line option --cgroup --comppair --compself --csv --force --html --max-procs --metric --no-comppair --no-compself --no-csv --no-force --no-html --no-pdf --no-png --no-svg --out-dir --pdf --png --quantile --rels --svg --use-count --use-ratio -m -o -q -r INPUT_PATH seismic-listpos command line option --complement --force --max-fmut-pos --max-procs --no-complement --no-force INPUT_PATH seismic-mask command line option --brotli-level --erase-tmp --exact-unbias --force --keep-del --keep-discontig --keep-gu --keep-ins --keep-tmp --mask-coords --mask-del --mask-discontig --mask-gu --mask-ins --mask-mut --mask-polya --mask-pos --mask-pos-file --mask-pos-table --mask-primers --mask-read --mask-read-file --mask-read-table --mask-regions-file --max-fmut-pos --max-fmut-read --max-mask-iter --max-procs --min-finfo-read --min-mut-gap --min-ncov-read --min-ninfo-pos --no-force --no-mask-pos-table --no-mask-read-table --primer-gap --quick-unbias --quick-unbias-thresh --tmp-pfx -c -i -P -t INPUT_PATH seismic-relate command line option --ambindel --batch-size --brotli-level --clip-end3 --clip-end5 --erase-tmp --force --insert3 --insert5 --keep-tmp --max-procs --min-mapq --min-phred --min-reads --mix-strands --no-ambindel --no-force --no-overhangs --no-relate-pos-table --no-relate-read-table --no-write-read-names --out-dir --overhangs --phred-enc --relate-cx --relate-pos-table --relate-py --relate-read-table --rev-label --sep-strands --tmp-pfx --write-read-names -3 -5 -N -o -t FASTA INPUT_PATH seismic-renumct command line option --ct-pos-5 --force --inplace --max-procs --no-force --no-inplace --out-dir -c -o seismic-sim-clusts command line option --clust-conc --ct-file --force --max-procs --no-force -c -i seismic-sim-ends command line option --center-fmean --center-fvar --ct-file --force --length-fmean --length-fvar --max-procs --no-force -i seismic-sim-fastq command line option --force --fq-gzip --fq-text --max-procs --min-mut-gap --no-force --num-reads --paired-end --param-dir --profile-name --read-length --reverse-fraction --sample --single-end -d -n -P -s INPUT_PATH seismic-sim-fold command line option --erase-tmp --fold-constraint --fold-coords --fold-max --fold-md --fold-mfe --fold-percent --fold-primers --fold-regions-file --fold-sub --fold-temp --force --keep-tmp --max-procs --no-force --profile-name --sim-dir --tmp-pfx -f -o -P -t FASTA seismic-sim-muts command line option --ct-file --force --max-procs --no-force --pmut-paired --pmut-unpaired --vmut-paired --vmut-unpaired -i -p -u -v -w seismic-sim-params command line option --center-fmean --center-fvar --clust-conc --ct-file --force --length-fmean --length-fvar --max-procs --no-force --pmut-paired --pmut-unpaired --vmut-paired --vmut-unpaired -c -i -p -u -v -w seismic-sim-ref command line option --force --no-force --ref --reflen --refs --sim-dir -N -o -R -r seismic-sim-relate command line option --batch-size --brotli-level --force --max-procs --min-mut-gap --no-force --no-write-read-names --num-reads --paired-end --param-dir --profile-name --read-length --reverse-fraction --sample --single-end --write-read-names -d -n -P -s seismic-sim-total command line option --center-fmean --center-fvar --clust-conc --erase-tmp --fold-constraint --fold-coords --fold-max --fold-md --fold-mfe --fold-percent --fold-primers --fold-regions-file --fold-sub --fold-temp --force --fq-gzip --fq-text --keep-tmp --length-fmean --length-fvar --max-procs --min-mut-gap --no-force --num-reads --paired-end --pmut-paired --pmut-unpaired --profile-name --read-length --ref --reflen --refs --reverse-fraction --sample --sim-dir --single-end --tmp-pfx --vmut-paired --vmut-unpaired -c -f -n -N -o -P -p -R -r -s -t -u -v -w seismic-table command line option --cluster-abundance-table --cluster-pos-table --force --mask-pos-table --mask-read-table --max-procs --no-cluster-abundance-table --no-cluster-pos-table --no-force --no-mask-pos-table --no-mask-read-table --no-relate-pos-table --no-relate-read-table --no-verify-times --relate-pos-table --relate-read-table --verify-times INPUT_PATH seismic-test command line option --verbose -v seismic-wf command line option --all-pos --ambindel --barcode-end --barcode-start --batch-size --brotli-level --bt2-contain --bt2-D --bt2-discordant --bt2-dovetail --bt2-dpad --bt2-end-to-end --bt2-gbar --bt2-I --bt2-i --bt2-L --bt2-local --bt2-mixed --bt2-no-contain --bt2-no-discordant --bt2-no-dovetail --bt2-no-mixed --bt2-no-un --bt2-orient --bt2-R --bt2-score-min-e2e --bt2-score-min-loc --bt2-un --bt2-X --cgroup --clip-end3 --clip-end5 --clipped --cluster --cluster-abundance-table --cluster-pos-table --color --csv --demult-off --demult-on --demulti-overwrite --dmfastqx --dmfastqy --dmfastqz --draw --em-runs --em-thresh --erase-tmp --exact-unbias --export --f1r2-fwd --f1r2-rev --fastp --fastp-3 --fastp-5 --fastp-adapter-1 --fastp-adapter-2 --fastp-adapter-fasta --fastp-adapter-trimming --fastp-detect-adapter-for-pe --fastp-m --fastp-min-length --fastp-poly-g --fastp-poly-g-min-len --fastp-poly-x --fastp-poly-x-min-len --fastp-w --fastqx --fastqy --fastqz --fold --fold-constraint --fold-coords --fold-full --fold-max --fold-md --fold-mfe --fold-percent --fold-primers --fold-regions-file --fold-sub --fold-table --fold-temp --force --graph-abundance --graph-aucroll --graph-giniroll --graph-mhist --graph-mprof --graph-mutdist --graph-ncov --graph-poscorr --graph-roc --graph-tmprof --hist-bins --hist-margin --html --index-tolerance --insert3 --insert5 --jackpot --jackpot-conf-level --keep-del --keep-discontig --keep-gu --keep-ins --keep-tmp --mask-coords --mask-del --mask-discontig --mask-gu --mask-ins --mask-mut --mask-polya --mask-pos --mask-pos-file --mask-pos-table --mask-primers --mask-read --mask-read-file --mask-read-table --mask-regions-file --max-clusters --max-em-iter --max-fmut-pos --max-fmut-read --max-jackpot-quotient --max-loglike-vs-best --max-marcd-vs-best --max-mask-iter --max-pearson-run --max-procs --min-clusters --min-em-iter --min-finfo-read --min-mapq --min-marcd-run --min-mut-gap --min-ncov-read --min-ninfo-pos --min-pearson-vs-best --min-phred --min-reads --mismatch-tolerence --mix-strands --mutdist-null --no-ambindel --no-cluster --no-cluster-abundance-table --no-cluster-pos-table --no-color --no-csv --no-draw --no-export --no-fastp --no-fastp-3 --no-fastp-5 --no-fastp-adapter-trimming --no-fastp-detect-adapter-for-pe --no-fastp-poly-x --no-fold --no-force --no-graph-abundance --no-graph-aucroll --no-graph-giniroll --no-graph-mhist --no-graph-mprof --no-graph-mutdist --no-graph-ncov --no-graph-poscorr --no-graph-roc --no-graph-tmprof --no-html --no-jackpot --no-mask-pos-table --no-mask-read-table --no-mutdist-null --no-overhangs --no-pdf --no-png --no-relate-pos-table --no-relate-read-table --no-svg --no-verify-times --no-write-read-names --out-dir --overhangs --parallel-demultiplexing --pdf --phred-enc --png --primer-gap --quantile --quick-unbias --quick-unbias-thresh --refs-meta --relate-cx --relate-pos-table --relate-py --relate-read-table --rev-label --samples-meta --sep-strands --stop-best-k --struct-file --struct-num --svg --tmp-pfx --try-all-ks --unmasked-pos --verify-times --window --winmin --write-all-ks --write-best-k --write-read-names -3 -5 -c -e -f -i -k -N -n -o -P -q -R -S -t -w -x -X -y -Y -z -Z FASTA INPUT_PATH

seismicrna module seismicrna.align module seismicrna.align.fqunit module seismicrna.align.main module seismicrna.align.report module seismicrna.align.split module seismicrna.align.tests module seismicrna.align.tests.write_test module seismicrna.align.tests.xamgen_test module seismicrna.align.tests.xamops_test module seismicrna.align.write module seismicrna.align.xamops module seismicrna.cleanfa module seismicrna.cleanfa.cleanfa module seismicrna.cleanfa.main module seismicrna.cluster module seismicrna.cluster.batch module seismicrna.cluster.dataset module seismicrna.cluster.em module seismicrna.cluster.emk module seismicrna.cluster.io module seismicrna.cluster.jackpot module seismicrna.cluster.main module seismicrna.cluster.marginal module seismicrna.cluster.names module seismicrna.cluster.obsexp module seismicrna.cluster.params module seismicrna.cluster.report module seismicrna.cluster.summary module seismicrna.cluster.table module seismicrna.cluster.tests module seismicrna.cluster.tests.emk_test module seismicrna.cluster.tests.jackpot_test module seismicrna.cluster.tests.marginal_test module seismicrna.cluster.uniq module seismicrna.cluster.write module seismicrna.core module seismicrna.core.arg module seismicrna.core.arg.cli module seismicrna.core.arg.cmd module seismicrna.core.arg.default module seismicrna.core.arg.docdef module seismicrna.core.array module seismicrna.core.batch module seismicrna.core.batch.accum module seismicrna.core.batch.count module seismicrna.core.batch.ends module seismicrna.core.batch.index module seismicrna.core.batch.muts module seismicrna.core.batch.read module seismicrna.core.batch.tests module seismicrna.core.batch.tests.accum_test module seismicrna.core.batch.tests.count_test module seismicrna.core.batch.tests.ends_test module seismicrna.core.batch.tests.index_test module seismicrna.core.batch.tests.muts_test module seismicrna.core.dataset module seismicrna.core.error module seismicrna.core.extern module seismicrna.core.extern.depend module seismicrna.core.extern.shell module seismicrna.core.extern.tests module seismicrna.core.header module seismicrna.core.io module seismicrna.core.io.batch module seismicrna.core.io.brickle module seismicrna.core.io.file module seismicrna.core.io.seq module seismicrna.core.io.tests module seismicrna.core.io.tests.file_test module seismicrna.core.join module seismicrna.core.logs module seismicrna.core.mu module seismicrna.core.mu.compare module seismicrna.core.mu.dim module seismicrna.core.mu.frame module seismicrna.core.mu.measure module seismicrna.core.mu.nan module seismicrna.core.mu.scale module seismicrna.core.mu.tests module seismicrna.core.mu.tests.compare_test module seismicrna.core.mu.tests.dim_test module seismicrna.core.mu.tests.frame_test module seismicrna.core.mu.tests.measure_test module seismicrna.core.mu.tests.nan_test module seismicrna.core.mu.tests.scale_test module seismicrna.core.ngs module seismicrna.core.ngs.phred module seismicrna.core.ngs.tests module seismicrna.core.ngs.tests.phred_test module seismicrna.core.ngs.tests.xam_test module seismicrna.core.ngs.xam module seismicrna.core.path module seismicrna.core.random module seismicrna.core.rel module seismicrna.core.rel.code module seismicrna.core.rel.pattern module seismicrna.core.rel.tests module seismicrna.core.rel.tests.code_test module seismicrna.core.rel.tests.pattern_test module seismicrna.core.report module seismicrna.core.rna module seismicrna.core.rna.base module seismicrna.core.rna.convert module seismicrna.core.rna.ct module seismicrna.core.rna.db module seismicrna.core.rna.io module seismicrna.core.rna.pair module seismicrna.core.rna.profile module seismicrna.core.rna.roc module seismicrna.core.rna.state module seismicrna.core.rna.struct module seismicrna.core.rna.tests module seismicrna.core.rna.tests.db_test module seismicrna.core.rna.tests.pair_test module seismicrna.core.run module seismicrna.core.seq module seismicrna.core.seq.fasta module seismicrna.core.seq.refs module seismicrna.core.seq.region module seismicrna.core.seq.section module seismicrna.core.seq.tests module seismicrna.core.seq.tests.fasta_test module seismicrna.core.seq.tests.region_test module seismicrna.core.seq.tests.xna_test module seismicrna.core.seq.xna module seismicrna.core.stats module seismicrna.core.table module seismicrna.core.table.base module seismicrna.core.table.write module seismicrna.core.task module seismicrna.core.tests module seismicrna.core.tests.array_test module seismicrna.core.tests.header_test module seismicrna.core.tests.logs_test module seismicrna.core.tests.path_test module seismicrna.core.tests.random_test module seismicrna.core.tests.stats_test module seismicrna.core.tests.task_test module seismicrna.core.tests.unbias_test module seismicrna.core.tests.version_test module seismicrna.core.tmp module seismicrna.core.types module seismicrna.core.unbias module seismicrna.core.version module seismicrna.core.write module seismicrna.demult module seismicrna.demult.demultiplex module seismicrna.demult.main module seismicrna.draw module seismicrna.draw.draw module seismicrna.draw.main module seismicrna.ensembles module seismicrna.export module seismicrna.export.main module seismicrna.export.meta module seismicrna.export.web module seismicrna.fold module seismicrna.fold.datapath module seismicrna.fold.load module seismicrna.fold.main module seismicrna.fold.report module seismicrna.fold.rnastructure module seismicrna.graph module seismicrna.graph.abundance module seismicrna.graph.aucroll module seismicrna.graph.base module seismicrna.graph.cgroup module seismicrna.graph.color module seismicrna.graph.corroll module seismicrna.graph.dataset module seismicrna.graph.delprof module seismicrna.graph.giniroll module seismicrna.graph.hist module seismicrna.graph.histpos module seismicrna.graph.histread module seismicrna.graph.main module seismicrna.graph.mutdist module seismicrna.graph.onesource module seismicrna.graph.onestruct module seismicrna.graph.onetable module seismicrna.graph.poscorr module seismicrna.graph.pospair module seismicrna.graph.profile module seismicrna.graph.rel module seismicrna.graph.roc module seismicrna.graph.roll module seismicrna.graph.scatter module seismicrna.graph.snrroll module seismicrna.graph.statroll module seismicrna.graph.table module seismicrna.graph.trace module seismicrna.graph.twotable module seismicrna.join module seismicrna.lists module seismicrna.lists.listpos module seismicrna.lists.lists module seismicrna.main module seismicrna.mask module seismicrna.mask.batch module seismicrna.mask.dataset module seismicrna.mask.io module seismicrna.mask.main module seismicrna.mask.report module seismicrna.mask.table module seismicrna.mask.tests module seismicrna.mask.tests.main_test module seismicrna.mask.write module seismicrna.migrate module seismicrna.pool module seismicrna.relate module seismicrna.relate.aux module seismicrna.relate.aux.cigarop module seismicrna.relate.aux.infer module seismicrna.relate.aux.iterread module seismicrna.relate.aux.iterrel module seismicrna.relate.aux.tests module seismicrna.relate.aux.tests.cigarop_test module seismicrna.relate.aux.tests.infer_test module seismicrna.relate.aux.tests.iterrel_test module seismicrna.relate.batch module seismicrna.relate.cx module seismicrna.relate.dataset module seismicrna.relate.io module seismicrna.relate.main module seismicrna.relate.py module seismicrna.relate.py.ambindel module seismicrna.relate.py.cigar module seismicrna.relate.py.encode module seismicrna.relate.py.error module seismicrna.relate.py.relate module seismicrna.relate.py.tests module seismicrna.relate.py.tests.ambindel_test module seismicrna.relate.py.tests.cigar_test module seismicrna.relate.py.tests.encode_test module seismicrna.relate.report module seismicrna.relate.sam module seismicrna.relate.sim module seismicrna.relate.strands module seismicrna.relate.table module seismicrna.relate.tests module seismicrna.relate.tests.main_test module seismicrna.relate.tests.relate_test module seismicrna.relate.tests.sam_test module seismicrna.relate.write module seismicrna.renumct module seismicrna.renumct.main module seismicrna.sim module seismicrna.sim.clusts module seismicrna.sim.ends module seismicrna.sim.fastq module seismicrna.sim.fold module seismicrna.sim.main module seismicrna.sim.muts module seismicrna.sim.params module seismicrna.sim.ref module seismicrna.sim.relate module seismicrna.sim.tests module seismicrna.sim.tests.ends_test module seismicrna.sim.total module seismicrna.table module seismicrna.test module seismicrna.test.main module seismicrna.tests module seismicrna.tests.ensembles_test module seismicrna.tests.wf_test module seismicrna.urls module seismicrna.wf module select() (seismicrna.core.header.Header method) semi_g_anomalies (seismicrna.cluster.em.EMRun property) separate_strands() (in module seismicrna.align.write) seq (seismicrna.core.rna.base.RNARegion property) (seismicrna.core.table.base.PositionTable property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) (seismicrna.relate.py.relate.SamRead attribute) seq_pos_to_index() (in module seismicrna.core.seq.region) seq_record (seismicrna.core.rna.base.RNARegion property) SeqColorMap (class in seismicrna.graph.color) Sequence_Obj (class in seismicrna.demult.demultiplex) set_config() (in module seismicrna.core.logs) setUp() (seismicrna.cluster.tests.jackpot_test.TestBootstrapJackpotScores method) (seismicrna.core.tests.path_test.TestSymlinkIfNeeded method) (seismicrna.mask.tests.main_test.TestMask method) (seismicrna.relate.tests.main_test.TestRelate method) (seismicrna.tests.ensembles_test.TestCalcRegions method) (seismicrna.tests.ensembles_test.TestEnsembles method) (seismicrna.tests.wf_test.TestWorkflow method) (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs method) ShellCommand (class in seismicrna.core.extern.shell) ShellCommandFailedError signature (seismicrna.core.header.ClustHeader property) (seismicrna.core.header.Header property) (seismicrna.core.header.RelHeader property) sim_data() (seismicrna.tests.ensembles_test.TestEnsembles class method) SIM_DIR (seismicrna.cluster.tests.jackpot_test.TestBootstrapJackpotScores attribute) (seismicrna.tests.ensembles_test.TestEnsembles attribute) (seismicrna.tests.wf_test.TestWorkflow attribute) (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) SIM_DIRS (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs attribute) sim_jackpot_quotient() (seismicrna.cluster.tests.jackpot_test.TestBootstrapJackpotScores method) sim_obs_exp() (in module seismicrna.cluster.jackpot) sim_pclust() (in module seismicrna.sim.clusts) sim_pclust_ct() (in module seismicrna.sim.clusts) sim_pends() (in module seismicrna.sim.ends) sim_pends_ct() (in module seismicrna.sim.ends) sim_pmut() (in module seismicrna.sim.muts) simulate() (seismicrna.relate.batch.ReadNamesBatch class method) (seismicrna.relate.batch.RelateBatch class method) simulate_batch() (in module seismicrna.relate.sim) simulate_batches() (in module seismicrna.relate.sim) simulate_cluster() (in module seismicrna.relate.sim) simulate_muts() (in module seismicrna.core.batch.muts) simulate_params() (in module seismicrna.core.tests.unbias_test) simulate_reads() (in module seismicrna.core.tests.unbias_test) simulate_relate() (in module seismicrna.relate.sim) simulate_segment_ends() (in module seismicrna.core.batch.ends) size (seismicrna.core.header.Header property) (seismicrna.core.seq.region.Region property) sort() (seismicrna.relate.py.ambindel.IndelPod method) sort_runs() (in module seismicrna.cluster.emk) sort_segment_ends() (in module seismicrna.core.batch.ends) sort_xam_cmd() (in module seismicrna.core.ngs.xam) split_fastq() (seismicrna.demult.demultiplex.super_fastq method) split_references() (in module seismicrna.align.write) split_xam_file() (in module seismicrna.align.split) START (seismicrna.core.logs.AnsiCode attribute) stat_func() (seismicrna.graph.giniroll.RollingGiniGraph class method) (seismicrna.graph.snrroll.RollingSNRGraph class method) (seismicrna.graph.statroll.RollingStatGraph class method) STATUS (seismicrna.core.logs.Level attribute) status() (seismicrna.core.logs.Logger method) stochastic_round() (in module seismicrna.core.random) Stream (class in seismicrna.core.logs) stream (seismicrna.core.logs.ConsoleStream property) (seismicrna.core.logs.FileStream property) (seismicrna.core.logs.Stream property) struct_reg (seismicrna.graph.onestruct.StructOneTableGraph property) StructOneTableGraph (class in seismicrna.graph.onestruct) StructOneTableRunner (class in seismicrna.graph.onestruct) StructOneTableWriter (class in seismicrna.graph.onestruct) subopt_indexes() (seismicrna.cluster.emk.EMRunsK method) subregion() (seismicrna.core.rna.base.RNARegion method) (seismicrna.core.seq.region.Region method) summarize() (seismicrna.cluster.emk.EMRunsK method) super_fastq (class in seismicrna.demult.demultiplex) super_write_fastqs() (seismicrna.demult.demultiplex.super_fastq method) symlink_if_needed() (in module seismicrna.core.path)

T

t (seismicrna.core.rel.pattern.HalfRelPattern attribute) t_or_u() (seismicrna.core.seq.xna.XNA class method) Table (class in seismicrna.core.table.base) table (seismicrna.draw.draw.RNArtistRun property) (seismicrna.graph.mutdist.MutationDistanceGraph property) (seismicrna.graph.onetable.OneTableWriter property) table1 (seismicrna.graph.twotable.TwoTableWriter property) table2 (seismicrna.graph.twotable.TwoTableWriter property) table_class (seismicrna.draw.draw.RNArtistRun property) table_classes (seismicrna.draw.draw.RNArtistRun property) table_file (seismicrna.draw.draw.RNArtistRun property) table_loader (seismicrna.draw.draw.RNArtistRun property) table_log_obs_exp() (in module seismicrna.cluster.obsexp) table_to_dict() (in module seismicrna.core.rna.pair) table_to_pairs() (in module seismicrna.core.rna.pair) table_types() (seismicrna.core.table.write.Tabulator class method) (seismicrna.mask.table.MaskTabulator class method) (seismicrna.relate.table.RelateTabulator class method) TableGraph (class in seismicrna.graph.table) TableLoader (class in seismicrna.relate.table) TableRunner (class in seismicrna.graph.table) TableWriter (class in seismicrna.core.table.write) (class in seismicrna.graph.table) tabulate() (in module seismicrna.cluster.summary) (in module seismicrna.table) tabulate_attr() (in module seismicrna.cluster.summary) Tabulator (class in seismicrna.core.table.write) tabulator (seismicrna.graph.mutdist.MutationDistanceGraph property) TallDataset (class in seismicrna.core.dataset) Task (class in seismicrna.core.task) TASK (seismicrna.core.logs.Level attribute) task() (seismicrna.core.logs.Logger method) tearDown() (seismicrna.cluster.tests.jackpot_test.TestBootstrapJackpotScores method) (seismicrna.core.tests.path_test.TestSymlinkIfNeeded method) (seismicrna.mask.tests.main_test.TestMask method) (seismicrna.relate.tests.main_test.TestRelate method) (seismicrna.tests.ensembles_test.TestCalcRegions method) (seismicrna.tests.ensembles_test.TestEnsembles method) (seismicrna.tests.wf_test.TestWorkflow method) (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs method) test_0() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_0_clusters() (seismicrna.cluster.tests.emk_test.TestAssignClusterings method) test_0_flags_bam() (seismicrna.align.tests.xamops_test.TestFlagsCmds method) test_0_flags_none() (seismicrna.align.tests.xamops_test.TestFlagsCmds method) test_0_positions() (seismicrna.cluster.tests.emk_test.TestAssignClusterings method) (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_0_positions_weighted() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_0_reads() (seismicrna.core.batch.tests.count_test.TestCalcUniqReadWeights method) test_0_segments() (seismicrna.core.batch.tests.ends_test.TestCountReadsSegments method) test_0d() (seismicrna.core.tests.array_test.TestFindDims method) test_0d_1dim() (seismicrna.core.tests.array_test.TestFindDims method) test_0d_none() (seismicrna.core.tests.array_test.TestFindDims method) test_0d_nonzero() (seismicrna.core.tests.array_test.TestFindDims method) test_0d_nonzero_extra() (seismicrna.core.tests.array_test.TestFindDims method) test_0x0() (seismicrna.core.tests.unbias_test.TestSlicePEnds method) (seismicrna.core.tests.unbias_test.TestTriuNorm method) test_0x0x1() (seismicrna.core.tests.unbias_test.TestTriuNorm method) test_1_cluster() (seismicrna.cluster.tests.emk_test.TestAssignClusterings method) test_1_dim() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEndsAuto method) test_1_flag_bam() (seismicrna.align.tests.xamops_test.TestFlagsCmds method) test_1_flag_none() (seismicrna.align.tests.xamops_test.TestFlagsCmds method) test_1_position() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_1_proc() (seismicrna.core.tests.task_test.TestCalcPoolSize method) test_1_read() (seismicrna.core.batch.tests.count_test.TestCalcUniqReadWeights method) test_1_segment() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) (seismicrna.core.batch.tests.ends_test.TestFindContiguousReads method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd3s method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd5s method) (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_1_segment_all_covered() (seismicrna.core.batch.tests.ends_test.TestCheckNoCoverageReads method) test_1_segment_none_covered() (seismicrna.core.batch.tests.ends_test.TestCheckNoCoverageReads method) test_1_segment_redundant() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_1_segment_redundant_weighted() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_1_segment_weighted() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) test_1_series_size_1_min_0_excl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_1_series_size_1_min_0_incl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_1_series_size_1_min_1_excl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_1_series_size_1_min_1_incl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_1_series_size_2_min_1_excl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_1_series_size_2_min_1_incl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_1_series_size_2_min_2_excl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_1_series_size_2_min_2_incl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_1_task() (seismicrna.core.tests.task_test.TestCalcPoolSize method) test_1d() (seismicrna.core.mu.tests.measure_test.TestCalcSignalNoise method) (seismicrna.core.tests.array_test.TestFindDims method) (seismicrna.core.tests.array_test.TestGetLength method) test_1d_0dim_none() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_1d_crossed() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_1d_separate() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_1dim_none() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_2d_congruent() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_2d_crossed() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_2dim() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_2dim_none() (seismicrna.core.tests.array_test.TestFindDims method) test_1d_nonzero() (seismicrna.core.tests.array_test.TestFindDims method) test_1pos() (seismicrna.cluster.tests.marginal_test.TestMarginalResps method) test_1pos_2clusters() (seismicrna.cluster.tests.marginal_test.TestMarginalResps method) test_1x1() (seismicrna.core.tests.unbias_test.TestTriuDiv method) (seismicrna.core.tests.unbias_test.TestTriuDot method) (seismicrna.core.tests.unbias_test.TestTriuMul method) (seismicrna.core.tests.unbias_test.TestTriuNorm method) (seismicrna.core.tests.unbias_test.TestTriuSum method) test_1x1x1() (seismicrna.core.tests.unbias_test.TestTriuDiv method) (seismicrna.core.tests.unbias_test.TestTriuDot method) (seismicrna.core.tests.unbias_test.TestTriuMul method) (seismicrna.core.tests.unbias_test.TestTriuNorm method) (seismicrna.core.tests.unbias_test.TestTriuSum method) test_1x1x2() (seismicrna.core.tests.unbias_test.TestTriuCumSum method) (seismicrna.core.tests.unbias_test.TestTriuNorm method) (seismicrna.core.tests.unbias_test.TestTriuSum method) test_2_dim() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEndsAuto method) test_2_flags_bam() (seismicrna.align.tests.xamops_test.TestFlagsCmds method) test_2_flags_none() (seismicrna.align.tests.xamops_test.TestFlagsCmds method) test_2_reads_1_uniq() (seismicrna.core.batch.tests.count_test.TestCalcUniqReadWeights method) test_2_reads_2_uniq() (seismicrna.core.batch.tests.count_test.TestCalcUniqReadWeights method) test_2_segments_all_covered() (seismicrna.core.batch.tests.ends_test.TestCheckNoCoverageReads method) test_2_segments_half_covered() (seismicrna.core.batch.tests.ends_test.TestCheckNoCoverageReads method) test_2_segments_mask() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) (seismicrna.core.batch.tests.ends_test.TestFindContiguousReads method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd3s method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd5s method) (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_2_segments_nomask() (seismicrna.core.batch.tests.count_test.TestCalcCoverage method) (seismicrna.core.batch.tests.ends_test.TestFindContiguousReads method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd3s method) (seismicrna.core.batch.tests.ends_test.TestFindReadEnd5s method) (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_2_segments_none_covered() (seismicrna.core.batch.tests.ends_test.TestCheckNoCoverageReads method) test_2_segments_unmask() (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_2_series_size_1_min_0_excl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_2_series_size_1_min_0_incl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_2_series_size_1_min_1_excl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_2_series_size_1_min_1_incl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_2_series_size_2_min_0_excl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_2_series_size_2_min_0_incl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_2_series_size_2_min_1_excl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_2_series_size_2_min_1_incl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_2_series_size_2_min_2_excl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_2_series_size_2_min_2_incl_nan() (seismicrna.core.seq.tests.region_test.TestGetWindows method) test_2d() (seismicrna.core.mu.tests.measure_test.TestCalcSignalNoise method) (seismicrna.core.tests.array_test.TestFindDims method) (seismicrna.core.tests.unbias_test.TestCalcRectangularSum method) (seismicrna.core.tests.unbias_test.TestTriuLog method) test_2d_1dim_none() (seismicrna.core.tests.array_test.TestFindDims method) test_2d_2d_congruent() (seismicrna.core.tests.array_test.TestFindDims method) test_2d_2d_crossed() (seismicrna.core.tests.array_test.TestFindDims method) test_2d_nonzero() (seismicrna.core.tests.array_test.TestFindDims method) test_2pos_gap0() (seismicrna.cluster.tests.marginal_test.TestMarginalResps method) test_2pos_gap0_2clusters() (seismicrna.cluster.tests.marginal_test.TestMarginalResps method) test_2pos_gap1() (seismicrna.cluster.tests.marginal_test.TestMarginalResps method) test_2pos_masked0() (seismicrna.cluster.tests.marginal_test.TestMarginalResps method) test_2pos_masked1() (seismicrna.cluster.tests.marginal_test.TestMarginalResps method) test_2x2() (seismicrna.core.tests.unbias_test.TestTriuCumSum method) (seismicrna.core.tests.unbias_test.TestTriuDiv method) (seismicrna.core.tests.unbias_test.TestTriuDot method) (seismicrna.core.tests.unbias_test.TestTriuMul method) (seismicrna.core.tests.unbias_test.TestTriuNorm method) (seismicrna.core.tests.unbias_test.TestTriuSum method) test_2x2_zero() (seismicrna.core.tests.unbias_test.TestTriuNorm method) test_2x2x1() (seismicrna.core.tests.unbias_test.TestTriuCumSum method) (seismicrna.core.tests.unbias_test.TestTriuNorm method) (seismicrna.core.tests.unbias_test.TestTriuSum method) test_2x2x2() (seismicrna.core.tests.unbias_test.TestTriuCumSum method) (seismicrna.core.tests.unbias_test.TestTriuDiv method) (seismicrna.core.tests.unbias_test.TestTriuDot method) (seismicrna.core.tests.unbias_test.TestTriuMul method) (seismicrna.core.tests.unbias_test.TestTriuNorm method) (seismicrna.core.tests.unbias_test.TestTriuSum method) test_2x2x2_zero() (seismicrna.core.tests.unbias_test.TestTriuNorm method) test_2x2x2x2() (seismicrna.core.tests.unbias_test.TestTriuNorm method) (seismicrna.core.tests.unbias_test.TestTriuSum method) test_2x2x2x2_zero() (seismicrna.core.tests.unbias_test.TestTriuNorm method) test_3d() (seismicrna.core.tests.unbias_test.TestCalcRectangularSum method) (seismicrna.core.tests.unbias_test.TestTriuLog method) test_3x3() (seismicrna.core.tests.unbias_test.TestTriuCumSum method) test_4nt_2ins() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_4nt_2ins_paired() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_5nt_2ins() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_6nt_2ins() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_7nt_0ins() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_8nt_0ins() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_a() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_aa_insert3() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_aa_insert5() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_abstract() (seismicrna.core.tests.header_test.TestHeader method) test_abstract_base_class() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_abut() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_add_mask() (seismicrna.core.seq.tests.region_test.TestRegionAddMask method) test_add_mask_complement() (seismicrna.core.seq.tests.region_test.TestRegionAddMask method) test_add_mask_invalid() (seismicrna.core.seq.tests.region_test.TestRegionAddMask method) test_add_overlapping_masks() (seismicrna.core.seq.tests.region_test.TestRegionAddMask method) test_add_unordered_mask() (seismicrna.core.seq.tests.region_test.TestRegionAddMask method) test_agg_insert3() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_agg_insert5() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_all() (seismicrna.core.tests.header_test.TestMakeHeader method) test_all_0() (seismicrna.core.tests.unbias_test.TestTriuCumSum method) test_all_1() (seismicrna.core.tests.unbias_test.TestTriuCumSum method) test_all_equal_1d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_all_equal_2d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_all_match() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_all_match_n() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_all_matches() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_all_zero() (seismicrna.core.tests.unbias_test.TestTriuSum method) test_all_zero_1d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_all_zero_2d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_allc() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) (seismicrna.core.rel.tests.pattern_test.TestRelPattern method) test_alph() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_ambig_delet_low_qual() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_array() (seismicrna.core.mu.tests.nan_test.TestAutoRemoveNaN method) (seismicrna.core.mu.tests.nan_test.TestAutoRemovesNaN method) test_array0d() (seismicrna.core.mu.tests.compare_test.TestCalcArcsineDistance method) (seismicrna.core.mu.tests.compare_test.TestCalcCoeffDeterm method) (seismicrna.core.mu.tests.compare_test.TestCalcMeanAbsFoldChangeOdds method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.compare_test.TestCalcSumAbsDiffLogOdds method) (seismicrna.core.mu.tests.dim_test.TestCountPos method) (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) test_array1d() (seismicrna.core.mu.tests.compare_test.TestCalcArcsineDistance method) (seismicrna.core.mu.tests.compare_test.TestCalcCoeffDeterm method) (seismicrna.core.mu.tests.compare_test.TestCalcMeanAbsFoldChangeOdds method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.compare_test.TestCalcSumAbsDiffLogOdds method) (seismicrna.core.mu.tests.dim_test.TestCountPos method) (seismicrna.core.mu.tests.dim_test.TestCountsPos method) (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.nan_test.TestNoNaN method) (seismicrna.core.mu.tests.nan_test.TestRemoveNaNs method) (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) test_array1d_all_nan() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_array1d_empty() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_array1d_nan() (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) test_array1d_some_nan() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_array2d() (seismicrna.core.mu.tests.compare_test.TestCalcArcsineDistance method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.dim_test.TestCountPos method) (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.nan_test.TestNoNaN method) (seismicrna.core.mu.tests.nan_test.TestRemoveNaNs method) (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) test_array2d_one_col_nan() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_array2d_one_row_nan() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_array3d() (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) test_array_all_equal() (seismicrna.cluster.tests.jackpot_test.TestCalcSemiGAnomaly method) test_array_all_unequal() (seismicrna.cluster.tests.jackpot_test.TestCalcSemiGAnomaly method) test_array_array() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_array_dataframe() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_array_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_array_index_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_array_ints() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_array_none() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_array_series() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_array_series_dataframe() (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) test_array_series_dataframe_mismatched() (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) test_arrays() (seismicrna.core.mu.tests.scale_test.TestWinsorize method) test_as_match() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_as_plain() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_average() (seismicrna.core.batch.tests.count_test.TestCalcCountPerPos method) (seismicrna.core.batch.tests.count_test.TestCalcCountPerRead method) (seismicrna.core.batch.tests.count_test.TestCalcRelsPerPos method) (seismicrna.core.batch.tests.count_test.TestCalcRelsPerRead method) test_average_prefix() (seismicrna.core.tests.header_test.TestConstants method) test_base_name() (seismicrna.core.seq.tests.region_test.TestConstants method) test_bases_muts() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_batch_size_1() (seismicrna.relate.tests.main_test.TestRelatePaired method) (seismicrna.relate.tests.main_test.TestRelateSingle method) test_batch_size_3() (seismicrna.relate.tests.main_test.TestRelateSingle method) test_batch_size_4() (seismicrna.relate.tests.main_test.TestRelatePaired method) test_batch_size_5() (seismicrna.relate.tests.main_test.TestRelatePaired method) test_batch_size_6() (seismicrna.relate.tests.main_test.TestRelatePaired method) test_blank() (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) test_blank_name() (seismicrna.core.seq.tests.fasta_test.TestWriteFasta method) test_bool() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_both_blank() (seismicrna.relate.tests.relate_test.TestMergeMates method) test_both_ones() (seismicrna.core.mu.tests.compare_test.TestCalcArcsineDistance method) test_both_reads() (seismicrna.relate.tests.relate_test.TestMergeMates method) test_both_zeros() (seismicrna.core.mu.tests.compare_test.TestCalcArcsineDistance method) test_c() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_calc_inverse() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_fwd() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_fwd_max() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_fwd_max_default() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_rev() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_rev_max() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_fill_rev_max_default() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_inverse_max() (seismicrna.core.tests.array_test.TestCalcInverse method) test_calc_p_clust_given_ends_noclose() (seismicrna.core.tests.unbias_test.TestCalcPClustGivenEndsNoClose method) test_calc_p_ends_given_noclose() (seismicrna.core.tests.unbias_test.TestCalcPEndsGivenNoClose method) test_calc_p_ends_given_observed() (seismicrna.core.tests.unbias_test.TestCalcPEndsObserved method) test_center_fvar_0_length_fvar_0() (seismicrna.sim.tests.ends_test.TestSimPEnds method) test_cigar_align_valid() (seismicrna.relate.py.tests.cigar_test.TestParseCigar method) test_cigar_init_invalid() (seismicrna.relate.aux.tests.cigarop_test.TestCigarOp method) test_cigar_init_valid() (seismicrna.relate.aux.tests.cigarop_test.TestCigarOp method) test_cigar_lengthen() (seismicrna.relate.aux.tests.cigarop_test.TestCigarOp method) test_cigar_m_aln_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_m_del_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_m_ins_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_m_mat_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_m_scl_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_m_sub_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_match_subst_valid() (seismicrna.relate.aux.tests.cigarop_test.TestCountCigarMuts method) (seismicrna.relate.py.tests.cigar_test.TestParseCigar method) test_cigar_str() (seismicrna.relate.aux.tests.cigarop_test.TestCigarOp method) test_cigar_xeq_aln_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_xeq_del_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_xeq_ins_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_xeq_mat_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_xeq_scl_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_cigar_xeq_sub_valid() (seismicrna.relate.aux.tests.cigarop_test.TestFindCigarOpPosRead method) test_clip() (seismicrna.relate.tests.main_test.TestRelatePaired method) (seismicrna.relate.tests.main_test.TestRelateSingle method) test_clust() (seismicrna.core.tests.header_test.TestParseHeader method) test_clust_name() (seismicrna.core.tests.header_test.TestConstants method) test_cluster_2_batches() (seismicrna.core.batch.tests.accum_test.TestAccumulateBatches method) test_cluster_prefix() (seismicrna.core.tests.header_test.TestConstants method) test_clustered() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_clusters() (seismicrna.core.batch.tests.count_test.TestCalcCountPerPos method) (seismicrna.core.batch.tests.count_test.TestCalcRelsPerPos method) (seismicrna.core.tests.unbias_test.TestCalcPMutGivenSpanNoClose method) (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds method) test_clustheaders() (seismicrna.core.tests.header_test.TestEqualHeaders method) test_clusts() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_compile_decompile() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_compile_example() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_comps() (seismicrna.core.mu.tests.compare_test.TestGetComp method) test_conflicting_pair_1() (seismicrna.core.rna.tests.pair_test.TestPairsToDict method) (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) test_conflicting_pair_2() (seismicrna.core.rna.tests.pair_test.TestPairsToDict method) (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) test_contain() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_contain_flush3() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_contain_flush5() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_contain_flush53() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_contains() (seismicrna.core.seq.tests.xna_test.TestDNA method) test_contiguous() (seismicrna.core.mu.tests.compare_test.TestCompareWindows method) test_copy() (seismicrna.core.seq.tests.region_test.TestRegionCopy method) test_dangling_closer() (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_dangling_opener() (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_dataframe() (seismicrna.core.mu.tests.compare_test.TestCalcArcsineDistance method) (seismicrna.core.mu.tests.compare_test.TestCalcCoeffDeterm method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.dim_test.TestCountPos method) (seismicrna.core.mu.tests.dim_test.TestCountsPos method) (seismicrna.core.mu.tests.frame_test.TestReframe method) (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.nan_test.TestNoNaN method) (seismicrna.core.mu.tests.nan_test.TestRemoveNaNs method) (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) (seismicrna.core.mu.tests.scale_test.TestWinsorize method) test_dataframe_array() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_dataframe_dataframe() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_decode() (seismicrna.core.ngs.tests.phred_test.TestDecode method) test_decompile_example() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_deep_pairs() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_defaults() (seismicrna.core.tests.logs_test.TestSetConfig method) test_delete_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_delete_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_derived_codes() (seismicrna.core.rel.tests.code_test.TestConstants method) test_dict_str_dna_rna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_diff_end3() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_diff_end5() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_diff_full() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_diff_lengths() (seismicrna.core.tests.array_test.TestEnsureSameLength method) test_diff_mask_name() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_diff_mask_positions() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_diff_name() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_diff_names() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_diff_ref() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_diff_refs() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_diff_seq() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_diff_seq5() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_diff_seqs() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_different_types() (seismicrna.core.tests.header_test.TestEqualHeaders method) test_distributed_1d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_drop_array() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_drop_dataframe() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_drop_series() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_duplicate_name() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_duplicated() (seismicrna.core.tests.header_test.TestValidateKs method) test_duplicates() (seismicrna.core.tests.header_test.TestDeduplicateRels method) test_empty() (seismicrna.core.mu.tests.dim_test.TestCountsPosConsensus method) (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) (seismicrna.core.rna.tests.pair_test.TestDictToTable method) (seismicrna.core.rna.tests.pair_test.TestPairsToDict method) (seismicrna.core.rna.tests.pair_test.TestTableToDict method) (seismicrna.core.rna.tests.pair_test.TestTableToPairs method) (seismicrna.core.seq.tests.region_test.TestGetWindows method) (seismicrna.core.tests.array_test.TestCalcInverse method) (seismicrna.core.tests.array_test.TestFindDims method) (seismicrna.core.tests.header_test.TestDeduplicateRels method) (seismicrna.core.tests.header_test.TestListKsClusts method) (seismicrna.core.tests.header_test.TestParseHeader method) (seismicrna.core.tests.header_test.TestValidateKs method) (seismicrna.relate.tests.relate_test.TestMergeMates method) test_empty_1d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) (seismicrna.core.mu.tests.measure_test.TestCalcSignalNoise method) test_empty_invalid() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_empty_max() (seismicrna.core.tests.array_test.TestCalcInverse method) test_encode() (seismicrna.core.ngs.tests.phred_test.TestEncode method) test_encode_relate_hi_qual() (seismicrna.relate.py.tests.encode_test.TestEncodeRelate method) test_encode_relate_lo_qual() (seismicrna.relate.py.tests.encode_test.TestEncodeRelate method) test_equal() (seismicrna.core.mu.tests.dim_test.TestCountsPosConsensus method) (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) (seismicrna.core.rel.tests.pattern_test.TestRelPattern method) (seismicrna.core.tests.unbias_test.TestTriuAllClose method) test_equal_dna_dna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_equal_full() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_equal_mask() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_equal_part() (seismicrna.core.seq.tests.region_test.TestRegionEqual method) test_equal_rna_rna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_erase_config() (seismicrna.core.tests.logs_test.TestEraseConfig method) test_error_cigar_adj_ins_del() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_consecutive() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_del_first_rel() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_del_last_rel() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_empty() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_ins_first_rel() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_ins_last_rel() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_missing() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_op_read_diff() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_op_ref_long() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_op_ref_zero() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_parse() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_cigar_soft_clips() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_flag_large() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_flag_missing() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_flag_parse() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_line_improper_flag_proper() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_line_paired_flag_unpaired() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_line_unpaired_flag_paired() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_mapq() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_mapq_insufficient() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_mapq_missing() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_name_missing() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_pos_large() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_pos_missing() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_pos_parse() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_pos_zero() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_qual_missing() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_read_missing() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_read_qual_diff() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_ref_mismatch() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_error_ref_missing() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_example_1() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_example_2() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_example_3() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_exc_info() (seismicrna.core.tests.logs_test.TestExcInfo method) test_excess_pseudoknot() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_explicit_sum() (seismicrna.core.tests.unbias_test.TestTriuCumSum method) test_extra_index_names() (seismicrna.core.tests.header_test.TestParseHeader method) test_extra_values() (seismicrna.core.tests.header_test.TestParseHeader method) test_f1r2_paired_mixed() (seismicrna.align.tests.write_test.TestCalcFlags method) test_f1r2_paired_unmixed() (seismicrna.align.tests.write_test.TestCalcFlags method) test_f1r2_single() (seismicrna.align.tests.write_test.TestCalcFlags method) test_f2r1_paired_mixed() (seismicrna.align.tests.write_test.TestCalcFlags method) test_f2r1_paired_unmixed() (seismicrna.align.tests.write_test.TestCalcFlags method) test_f2r1_single() (seismicrna.align.tests.write_test.TestCalcFlags method) test_find_gu() (seismicrna.core.seq.tests.region_test.TestRegionMaskGU method) test_find_polya() (seismicrna.core.seq.tests.region_test.TestRegionMaskPolyA method) test_fits() (seismicrna.core.rel.tests.pattern_test.TestRelPattern method) test_fits_allc() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_fits_muts() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_fits_refs() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_fits_subs() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_float_array() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_float_arrays() (seismicrna.core.tests.random_test.TestStochasticRound method) test_float_arrays_preserve_sum() (seismicrna.core.tests.random_test.TestStochasticRound method) test_float_clust() (seismicrna.core.tests.header_test.TestValidateKClust method) test_float_dataframe() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_float_equal() (seismicrna.cluster.tests.jackpot_test.TestCalcSemiGAnomaly method) (seismicrna.core.tests.unbias_test.TestTriuAllClose method) test_float_float() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_float_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_index_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_index_index_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_index_index_int() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_index_int() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_int_index() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_ints() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_k() (seismicrna.core.tests.header_test.TestValidateKClust method) test_float_none() (seismicrna.core.mu.tests.frame_test.TestReframe method) test_float_series() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_float_unequal() (seismicrna.cluster.tests.jackpot_test.TestCalcSemiGAnomaly method) (seismicrna.core.tests.unbias_test.TestTriuAllClose method) test_force() (seismicrna.core.seq.tests.fasta_test.TestWriteFasta method) test_format_default() (seismicrna.core.tests.version_test.TestFormatVersion method) test_format_fasta_name_line() (seismicrna.core.seq.tests.fasta_test.TestFormat method) test_format_fasta_record() (seismicrna.core.seq.tests.fasta_test.TestFormat method) test_format_fasta_seq_lines() (seismicrna.core.seq.tests.fasta_test.TestFormat method) test_format_notag() (seismicrna.core.tests.version_test.TestFormatVersion method) test_format_prtag() (seismicrna.core.tests.version_test.TestFormatVersion method) test_from_counts() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) (seismicrna.core.rel.tests.pattern_test.TestRelPattern method) test_from_report_format() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_full() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_full_blank_name() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_full_end3() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_full_end5() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_full_given_name() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_full_lengths() (seismicrna.core.seq.tests.region_test.TestRegionLength method) test_full_name() (seismicrna.core.seq.tests.region_test.TestConstants method) test_full_reads_no_muts() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_full_reads_no_muts_some_masked() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_full_region_full_length_sub() (seismicrna.core.seq.tests.region_test.TestSubregion method) test_full_region_full_sub() (seismicrna.core.seq.tests.region_test.TestSubregion method) test_full_region_full_sub_end3() (seismicrna.core.seq.tests.region_test.TestSubregion method) test_full_region_full_sub_end5() (seismicrna.core.seq.tests.region_test.TestSubregion method) test_full_region_full_sub_name() (seismicrna.core.seq.tests.region_test.TestSubregion method) test_g() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_gap() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_gap0() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap1_single_end3() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap1_single_end5() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap1_split0_quadruple() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap1_split1_double() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap1_split1_single_mid() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap1_split1_triple() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap1_split2() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap2_single_end3() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap2_single_end5() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap2_split0() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap2_split1() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap3_single_end3() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap3_single_end5() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap4_split0() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap4_split1() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_gap_le_zero_le_npos() (seismicrna.core.tests.unbias_test.TestAdjustMinGap method) test_generic_split() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_get_alphaset() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_get_comp() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_get_comptrans() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_get_config() (seismicrna.core.tests.logs_test.TestGetConfig method) test_get_mask() (seismicrna.core.seq.tests.region_test.TestRegionMaskNames method) test_get_nonalphaset() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_get_seismicrna_source_dir() (seismicrna.core.tests.path_test.TestGetSeismicRNASourceDir method) test_hashable_dna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_hashable_rna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_hyphenate() (seismicrna.core.seq.tests.region_test.TestHyphenateEnds method) test_ideal_jackpot() (seismicrna.cluster.tests.jackpot_test.TestBootstrapJackpotScores method) test_illegal_prefix() (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) test_illegal_suffix() (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) test_improper() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_index() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_inequality_min_num_edits() (seismicrna.align.tests.xamgen_test.TestAlignmentScoreParams method) test_inequality_subst_vs_indel() (seismicrna.align.tests.xamgen_test.TestAlignmentScoreParams method) test_infer() (seismicrna.core.tests.unbias_test.TestCalcParams method) test_insert3_end3_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert3_non_match_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert3_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert5_end5_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert5_non_match_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert5_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_insert_deletion_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_int_arrays() (seismicrna.core.tests.random_test.TestStochasticRound method) test_intersect() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_intersect_none() (seismicrna.core.rel.tests.pattern_test.TestRelPattern method) test_intersect_other() (seismicrna.core.rel.tests.pattern_test.TestRelPattern method) test_invalid_1() (seismicrna.core.tests.version_test.TestParseVersion method) test_invalid_2() (seismicrna.core.tests.version_test.TestParseVersion method) test_invalid_3() (seismicrna.core.tests.version_test.TestParseVersion method) test_invalid_4() (seismicrna.core.tests.version_test.TestParseVersion method) test_invalid_5() (seismicrna.core.tests.version_test.TestParseVersion method) test_invalid_bases() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_invalid_dim() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEndsAuto method) test_invalid_dup_1() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_invalid_empty_seq_1() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_invalid_empty_seq_2() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_invalid_empty_seq_3() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_invalid_full_0() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_invalid_greater_end_9() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_invalid_less_start_2() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_invalid_name() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) (seismicrna.core.seq.tests.fasta_test.TestWriteFasta method) test_invalid_noncontig() (seismicrna.core.seq.tests.region_test.TestIndexToSeq method) test_invalid_numeric() (seismicrna.core.tests.header_test.TestParseHeader method) test_invalid_pair() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) test_invalid_pos3() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_invalid_pos5() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_invalid_position() (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) (seismicrna.core.rna.tests.pair_test.TestPairsToDict method) test_invalid_position_1() (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) test_invalid_position_2() (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) test_invalid_quantiles() (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) test_invalid_seq() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_invalid_unsort_1() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_invert() (seismicrna.core.rel.tests.pattern_test.TestRelPattern method) (seismicrna.core.tests.stats_test.TestCalcBetaParams method) (seismicrna.core.tests.stats_test.TestCalcDirichletParams method) (seismicrna.core.tests.unbias_test.TestCalcPEnds method) (seismicrna.core.tests.unbias_test.TestCalcPMutGivenSpan method) test_is_acgt() (seismicrna.relate.py.tests.encode_test.TestIsACGT method) test_is_inverse() (seismicrna.core.tests.array_test.TestCalcInverse method) test_iter_clust_indexes() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_k_name() (seismicrna.core.tests.header_test.TestConstants method) test_kmers() (seismicrna.core.seq.tests.xna_test.TestDNA method) test_ks() (seismicrna.core.tests.header_test.TestListKsClusts method) (seismicrna.core.tests.header_test.TestMakeHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_ks_invalid() (seismicrna.core.tests.header_test.TestClustHeader method) test_ks_valid() (seismicrna.core.tests.header_test.TestClustHeader method) test_length_0() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds method) test_length_1() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds method) (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsAll method) test_length_2() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsAll method) test_length_2_diff() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) test_length_2_min_gap_1() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds method) test_length_2_same() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) test_length_3() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsAll method) test_length_3_diff_weights() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) test_length_3_min_gap_1() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds method) test_length_3_min_gap_2() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds method) test_length_3_same_weights() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) test_length_3_same_weights_int() (seismicrna.core.batch.tests.count_test.TestCountEndCoords method) test_length_4_min_gap_1() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds method) test_length_4_min_gap_2() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds method) test_length_4_min_gap_3() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds method) test_level_keys() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_level_names() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_levels() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) (seismicrna.core.tests.logs_test.TestLevels method) test_link_not_symlink() (seismicrna.core.tests.path_test.TestSymlinkIfNeeded method) test_link_valid() (seismicrna.core.tests.path_test.TestSymlinkIfNeeded method) test_link_wrong_symlink() (seismicrna.core.tests.path_test.TestSymlinkIfNeeded method) test_locate_0() (seismicrna.core.tests.array_test.TestLocateElements method) test_locate_1() (seismicrna.core.tests.array_test.TestLocateElements method) test_locate_2() (seismicrna.core.tests.array_test.TestLocateElements method) test_locate_invalid() (seismicrna.core.tests.array_test.TestLocateElements method) test_log_file() (seismicrna.core.tests.logs_test.TestSetConfig method) test_logger_class() (seismicrna.core.tests.logs_test.TestLoggerClass method) test_long_ambindels() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_low_qual() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_low_qual_invalid() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_low_qual_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_mask() (seismicrna.core.batch.tests.ends_test.TestMaskSegmentEnds method) (seismicrna.core.batch.tests.ends_test.TestMergeSegmentEnds method)

test_mask_2_batches() (seismicrna.core.batch.tests.accum_test.TestAccumulateBatches method) test_mask_all_muts_min_ncov_read_7() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_discontig() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_gu() (seismicrna.core.seq.tests.region_test.TestRegionMaskGU method) (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_gu_min_ncov_read_5() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_gu_min_ncov_read_6() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_list() (seismicrna.core.seq.tests.region_test.TestRegionMaskList method) test_mask_names() (seismicrna.core.seq.tests.region_test.TestRegionMaskNames method) test_mask_polya() (seismicrna.core.seq.tests.region_test.TestRegionMaskPolyA method) test_mask_polya_3() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_polya_4() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_pos() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_pos_all() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_pos_and_mask_pos_file() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_pos_file() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_pos_min_ncov_read_5() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_pos_min_ncov_read_6() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_pos_multiple() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_read() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_read_and_mask_read_file() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_mask_read_file() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_masked_bool() (seismicrna.core.seq.tests.region_test.TestRegionMasked method) test_masked_int() (seismicrna.core.seq.tests.region_test.TestRegionMasked method) test_masked_zero() (seismicrna.core.seq.tests.region_test.TestRegionMasked method) test_match() (seismicrna.core.batch.tests.ends_test.TestMatchReadsSegments method) test_meson_build() (seismicrna.core.tests.version_test.TestConsistentVersion method) test_min_finfo_read_1() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_min_gap_0() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenEnds method) test_min_ncov_read_6() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_min_ncov_read_7() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_min_ncov_read_8() (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_min_phred() (seismicrna.relate.tests.main_test.TestRelatePaired method) (seismicrna.relate.tests.main_test.TestRelateSingle method) test_min_reads() (seismicrna.relate.tests.main_test.TestRelateEmpty method) (seismicrna.relate.tests.main_test.TestRelatePaired method) (seismicrna.relate.tests.main_test.TestRelateSingle method) test_misformatted() (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) test_mismatch() (seismicrna.core.batch.tests.ends_test.TestMergeReadEnds method) test_missing_index_names() (seismicrna.core.tests.header_test.TestParseHeader method) test_missing_reverse_1() (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) test_missing_reverse_2() (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) test_missing_values() (seismicrna.core.tests.header_test.TestParseHeader method) test_modified_all() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_modified_ks() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_modified_ks_empty() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_modified_ks_none() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_modified_none() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_modified_nullified() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_modified_rels() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_modified_rels_empty() (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_modified_rels_none() (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_modules012_read120() (seismicrna.tests.ensembles_test.TestEnsembles method) test_modules012_read180() (seismicrna.tests.ensembles_test.TestEnsembles method) test_modules012_read60() (seismicrna.tests.ensembles_test.TestEnsembles method) test_modules02_read60() (seismicrna.tests.ensembles_test.TestEnsembles method) test_monopoly_1d() (seismicrna.core.mu.tests.measure_test.TestCalcGini method) test_more_clusters() (seismicrna.cluster.tests.emk_test.TestAssignClusterings method) test_more_muts() (seismicrna.core.tests.unbias_test.TestNoCloseMuts method) test_multi_marks() (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_multi_pseudoknot() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_multiple() (seismicrna.core.tests.task_test.TestCalcPoolSize method) test_muts() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) (seismicrna.core.rel.tests.pattern_test.TestRelPattern method) test_n() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_n_read() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_n_ref() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_n_segments_contig() (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_n_segments_discontig() (seismicrna.core.batch.tests.ends_test.TestSortSegmentEnds method) test_name_mark() (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) test_names() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_nan() (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) test_ncls1() (seismicrna.core.tests.unbias_test.TestCalcPClustGivenNoClose method) test_ncls2() (seismicrna.core.tests.unbias_test.TestCalcPClustGivenNoClose method) test_negative() (seismicrna.core.tests.array_test.TestCalcInverse method) test_negative_zero() (seismicrna.core.tests.header_test.TestValidateKClust method) test_nested() (seismicrna.core.rna.tests.pair_test.TestFindEnclosingPairs method) test_no_duplicates() (seismicrna.core.tests.header_test.TestDeduplicateRels method) test_no_log_color() (seismicrna.core.tests.logs_test.TestSetConfig method) test_no_muts() (seismicrna.core.tests.unbias_test.TestNoCloseMuts method) test_no_pairs() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) (seismicrna.core.rna.tests.pair_test.TestFindEnclosingPairs method) (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) test_no_raise_on_error() (seismicrna.core.tests.logs_test.TestLoggingRaiseOnError method) test_noargs() (seismicrna.relate.tests.main_test.TestRelateEmpty method) (seismicrna.relate.tests.main_test.TestRelatePaired method) (seismicrna.relate.tests.main_test.TestRelateSingle method) test_nocov_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_nomask() (seismicrna.core.batch.tests.ends_test.TestMaskSegmentEnds method) (seismicrna.core.batch.tests.ends_test.TestMergeSegmentEnds method) (seismicrna.mask.tests.main_test.TestMaskSingle1Sample1Batch method) test_non_array() (seismicrna.core.batch.tests.ends_test.TestCountReadsSegments method) test_none() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) (seismicrna.core.tests.header_test.TestMakeHeader method) test_none_2d() (seismicrna.core.tests.array_test.TestFindDims method) test_nonnumeric() (seismicrna.core.tests.header_test.TestParseHeader method) test_normal() (seismicrna.core.rna.tests.pair_test.TestDictToPairs method) (seismicrna.core.rna.tests.pair_test.TestDictToTable method) (seismicrna.core.rna.tests.pair_test.TestPairsToDict method) (seismicrna.core.rna.tests.pair_test.TestPairsToTable method) (seismicrna.core.rna.tests.pair_test.TestTableToDict method) (seismicrna.core.rna.tests.pair_test.TestTableToPairs method) test_not_equal_dna_rna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_not_equal_dna_str() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_not_equal_rna_str() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_np_type() (seismicrna.core.rel.tests.code_test.TestConstants method) test_npos0_ncls1() (seismicrna.core.tests.unbias_test.TestCalcPEndsGivenClustNoClose method) test_npos1_ncls0() (seismicrna.core.tests.unbias_test.TestCalcPEndsGivenClustNoClose method) test_npos1_ncls1() (seismicrna.core.tests.unbias_test.TestCalcPEndsGivenClustNoClose method) test_npos2_ncls1() (seismicrna.core.tests.unbias_test.TestCalcPEndsGivenClustNoClose method) test_npos_le_zero_le_gap() (seismicrna.core.tests.unbias_test.TestAdjustMinGap method) test_num_levels() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_one_degenerate() (seismicrna.core.seq.tests.xna_test.TestExpandDegenerateSeq method) test_one_full() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_one_full_named() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_one_half() (seismicrna.core.mu.tests.compare_test.TestCalcArcsineDistance method) test_one_improper() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) test_one_invalid() (seismicrna.core.seq.tests.region_test.TestGetSharedIndex method) test_one_k() (seismicrna.core.tests.header_test.TestListKsClusts method) test_one_masked() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_one_mut() (seismicrna.core.tests.unbias_test.TestNoCloseMuts method) test_one_pair() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_one_proper() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) test_one_single() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) test_one_slice() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_one_valid() (seismicrna.core.seq.tests.region_test.TestGetSharedIndex method) test_one_zero_allowed() (seismicrna.core.tests.header_test.TestValidateKClust method) test_other_dims() (seismicrna.core.tests.array_test.TestEnsureSameLength method) (seismicrna.core.tests.array_test.TestGetLength method) test_overhangs() (seismicrna.relate.tests.relate_test.TestMergeMates method) test_p_clust() (seismicrna.core.tests.unbias_test.TestCalcPClust method) test_p_noclose() (seismicrna.core.tests.unbias_test.TestCalcPNoClose method) test_p_noclose_given_clust() (seismicrna.core.tests.unbias_test.TestCalcPNoCloseGivenClust method) test_paired_improper() (seismicrna.relate.tests.sam_test.TestLineAttrs method) test_paired_marks() (seismicrna.core.rna.tests.db_test.TestPairedMarks method) test_paired_proper() (seismicrna.relate.tests.sam_test.TestLineAttrs method) test_paired_reads_masked_segments() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_paired_reads_no_muts() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_parse_default() (seismicrna.core.tests.version_test.TestParseVersion method) test_parse_notag() (seismicrna.core.tests.version_test.TestParseVersion method) test_parse_prtag_letter() (seismicrna.core.tests.version_test.TestParseVersion method) test_parse_prtag_letters() (seismicrna.core.tests.version_test.TestParseVersion method) test_parse_prtag_letters_numbers() (seismicrna.core.tests.version_test.TestParseVersion method) test_partial_lengths() (seismicrna.core.seq.tests.region_test.TestRegionLength method) test_partial_reads_muts() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_partial_reads_no_muts() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_partial_reads_no_muts_some_masked() (seismicrna.core.batch.tests.muts_test.TestCalcMutsMatrix method) test_partial_reflen_equal() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_reflen_greater() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_reflen_less() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_seq5_equal() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_seq5_greater() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_seq5_less() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_seq5_reflen() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_slice() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_slice_invalid_end3() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_slice_invalid_end5() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_slice_invalid_reflen() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_slice_invalid_seq5() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_partial_trunc_region_trunc_sub() (seismicrna.core.seq.tests.region_test.TestSubregion method) test_phreds() (seismicrna.core.ngs.tests.phred_test.TestConstants method) test_picto() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_pos_name() (seismicrna.core.seq.tests.region_test.TestConstants method) test_positive() (seismicrna.core.tests.header_test.TestFormatClustName method) (seismicrna.core.tests.header_test.TestListClusts method) (seismicrna.core.tests.header_test.TestListKClusts method) test_positive_invalid_dups() (seismicrna.core.tests.header_test.TestFormatClustNames method) test_positive_no_dups() (seismicrna.core.tests.header_test.TestFormatClustNames method) test_positive_positive() (seismicrna.core.tests.header_test.TestValidateKClust method) test_positive_valid_dups() (seismicrna.core.tests.header_test.TestFormatClustNames method) test_primary_codes() (seismicrna.core.rel.tests.code_test.TestConstants method) test_pseudoknot() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_pseudoknotted() (seismicrna.core.rna.tests.pair_test.TestFindEnclosingPairs method) test_quals() (seismicrna.core.ngs.tests.phred_test.TestConstants method) test_raise_on_error() (seismicrna.core.tests.logs_test.TestLoggingRaiseOnError method) (seismicrna.core.tests.logs_test.TestSetConfig method) test_random() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_range() (seismicrna.core.seq.tests.region_test.TestRegionRange method) test_range_int() (seismicrna.core.seq.tests.region_test.TestRegionRange method) test_range_one() (seismicrna.core.seq.tests.region_test.TestRegionRange method) test_re_patterns() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_read1() (seismicrna.relate.tests.relate_test.TestMergeMates method) test_read2() (seismicrna.relate.tests.relate_test.TestMergeMates method) test_read_marks() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_read_orientation() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_reduce_0() (seismicrna.core.mu.tests.frame_test.TestAutoReframe method) test_reduce_0_and_1() (seismicrna.core.mu.tests.frame_test.TestAutoReframe method) test_reduce_none() (seismicrna.core.mu.tests.frame_test.TestAutoReframe method) test_refs() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_region_length_larger() (seismicrna.tests.ensembles_test.TestCalcRegions method) test_region_min_overlap_25() (seismicrna.tests.ensembles_test.TestCalcRegions method) test_region_min_overlap_75() (seismicrna.tests.ensembles_test.TestCalcRegions method) test_region_not_divisible() (seismicrna.tests.ensembles_test.TestCalcRegions method) test_rel_index() (seismicrna.core.tests.header_test.TestParseHeader method) test_rel_index_invalid_name() (seismicrna.core.tests.header_test.TestParseHeader method) test_rel_index_repeated() (seismicrna.core.tests.header_test.TestParseHeader method) test_rel_index_valid_name() (seismicrna.core.tests.header_test.TestParseHeader method) test_rel_multiindex() (seismicrna.core.tests.header_test.TestParseHeader method) test_rel_name() (seismicrna.core.tests.header_test.TestConstants method) test_relate_1_batch() (seismicrna.core.batch.tests.accum_test.TestAccumulateBatches method) test_relate_2_batches() (seismicrna.core.batch.tests.accum_test.TestAccumulateBatches method) test_relclust() (seismicrna.core.tests.header_test.TestParseHeader method) test_relclustheaders() (seismicrna.core.tests.header_test.TestEqualHeaders method) test_relheaders() (seismicrna.core.tests.header_test.TestEqualHeaders method) test_rels() (seismicrna.core.tests.header_test.TestMakeHeader method) test_rels_duplicated() (seismicrna.core.tests.header_test.TestRelHeader method) test_rels_empty() (seismicrna.core.tests.header_test.TestRelHeader method) test_rels_normal() (seismicrna.core.tests.header_test.TestRelHeader method) test_repeat_pos3() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_repeat_pos5() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) test_repeated() (seismicrna.core.tests.array_test.TestCalcInverse method) test_restore_config_error() (seismicrna.core.tests.logs_test.TestRestoreConfig method) test_restore_config_no_error() (seismicrna.core.tests.logs_test.TestRestoreConfig method) test_reverse_complement() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_reverse_transcribe() (seismicrna.core.seq.tests.xna_test.TestRNA method) test_same_length() (seismicrna.core.tests.array_test.TestEnsureSameLength method) test_scipy_beta() (seismicrna.core.tests.stats_test.TestCalcBetaMV method) test_scipy_dirichlet() (seismicrna.core.tests.stats_test.TestCalcDirichletMV method) test_score_consistency() (seismicrna.align.tests.xamgen_test.TestAlignmentScoreParams method) test_select_clust() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_clusts() (seismicrna.core.tests.header_test.TestClustHeader method) test_select_extra() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_select_extra_emptystr() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_extra_none() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_extra_zero() (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_select_invalid() (seismicrna.core.tests.header_test.TestRelHeader method) test_select_invalid_clust() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_invalid_k() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_invalid_rel() (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_k() (seismicrna.core.tests.header_test.TestClustHeader method) test_select_k_clust_empty() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_k_clust_exist() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_ks() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) test_select_ks_clusts_exist() (seismicrna.core.tests.header_test.TestClustHeader method) test_select_none() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_select_one_rels() (seismicrna.core.tests.header_test.TestRelHeader method) test_select_rel() (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_select_two_rels() (seismicrna.core.tests.header_test.TestRelHeader method) test_seq_index_names() (seismicrna.core.seq.tests.region_test.TestConstants method) test_series() (seismicrna.core.mu.tests.compare_test.TestCalcArcsineDistance method) (seismicrna.core.mu.tests.compare_test.TestCalcPearson method) (seismicrna.core.mu.tests.compare_test.TestCalcSpearman method) (seismicrna.core.mu.tests.dim_test.TestCountPos method) (seismicrna.core.mu.tests.dim_test.TestCountsPos method) (seismicrna.core.mu.tests.frame_test.TestReframe method) (seismicrna.core.mu.tests.nan_test.TestAnyNaN method) (seismicrna.core.mu.tests.nan_test.TestNoNaN method) (seismicrna.core.mu.tests.nan_test.TestRemoveNaNs method) (seismicrna.core.mu.tests.nan_test.TestRemovesNaNs method) (seismicrna.core.mu.tests.scale_test.TestCalcQuantile method) (seismicrna.core.mu.tests.scale_test.TestCalcRanks method) (seismicrna.core.mu.tests.scale_test.TestNormalize method) (seismicrna.core.mu.tests.scale_test.TestWinsorize method) test_series_array() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_series_series() (seismicrna.core.mu.tests.frame_test.TestReframeLike method) test_set_str_dna_rna() (seismicrna.core.seq.tests.xna_test.TestXNA method) test_shallow_pairs() (seismicrna.core.rna.tests.db_test.TestFormatDbStructure method) (seismicrna.core.rna.tests.db_test.TestParseDbStructure method) test_signature() (seismicrna.core.tests.header_test.TestClustHeader method) (seismicrna.core.tests.header_test.TestRelClustHeader method) (seismicrna.core.tests.header_test.TestRelHeader method) test_sim_clusters() (seismicrna.cluster.tests.jackpot_test.TestSimClusters method) test_sim_reads() (seismicrna.cluster.tests.jackpot_test.TestSimReads method) test_simulated() (seismicrna.core.tests.unbias_test.TestCalcPMutGivenSpanNoClose method) test_single() (seismicrna.relate.tests.sam_test.TestLineAttrs method) test_size() (seismicrna.core.seq.tests.region_test.TestRegionUnmasked method) (seismicrna.core.tests.header_test.TestRelHeader method) test_slice() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_slice_3x3() (seismicrna.core.tests.unbias_test.TestSlicePEnds method) test_slice_5x5() (seismicrna.core.tests.unbias_test.TestSlicePEnds method) test_slice_end3_equal() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_slice_end3_greater() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_slice_end3_less() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_slice_end5_end3() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_slice_end5_end3_invalid() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_slice_end5_equal() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_slice_end5_greater() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_slice_end5_less() (seismicrna.core.seq.tests.region_test.TestRegionInit method) test_slice_lengths() (seismicrna.core.seq.tests.region_test.TestRegionLength method) test_soft_clips() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesSingle method) test_staggered() (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_subs_decodings() (seismicrna.relate.py.tests.encode_test.TestSubsCoding method) test_subs_encodings() (seismicrna.relate.py.tests.encode_test.TestSubsCoding method) test_subst_invalid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_subst_valid() (seismicrna.relate.aux.tests.infer_test.TestInferRead method) test_sum_positive() (seismicrna.core.tests.unbias_test.TestNormalize method) test_sum_zero() (seismicrna.core.tests.unbias_test.TestNormalize method) test_t() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_target_not_exist() (seismicrna.core.tests.path_test.TestSymlinkIfNeeded method) test_three_overlapping() (seismicrna.core.seq.tests.region_test.TestIntersect method) test_thresh0() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_thresh1() (seismicrna.core.tests.unbias_test.TestFindSplitPositions method) test_threshold_0() (seismicrna.core.tests.unbias_test.TestQuickUnbias method) test_threshold_0p001() (seismicrna.core.tests.unbias_test.TestQuickUnbias method) test_to_array() (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) test_to_report_format() (seismicrna.core.rel.tests.pattern_test.TestHalfRelPattern method) test_total_region_length_1() (seismicrna.tests.ensembles_test.TestCalcRegions method) test_transcribe() (seismicrna.core.seq.tests.xna_test.TestDNA method) test_tril() (seismicrna.core.tests.unbias_test.TestTriuAllClose method) test_triu() (seismicrna.core.tests.unbias_test.TestTriuAllClose method) test_trunc_region_full_sub() (seismicrna.core.seq.tests.region_test.TestSubregion method) test_trunc_region_trunc_sub() (seismicrna.core.seq.tests.region_test.TestSubregion method) test_two_degenerate() (seismicrna.core.seq.tests.xna_test.TestExpandDegenerateSeq method) test_two_disjoint() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_two_disjoint_refseq() (seismicrna.core.seq.tests.region_test.TestUnite method) test_two_disjoint_wrong_refseq() (seismicrna.core.seq.tests.region_test.TestUnite method) test_two_full() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_two_invalid() (seismicrna.core.seq.tests.region_test.TestGetSharedIndex method) test_two_masked() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_two_mated_improper() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) test_two_mated_improper_1() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) test_two_mated_improper_2() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) test_two_mated_proper() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) test_two_overlapping() (seismicrna.core.seq.tests.region_test.TestIntersect method) (seismicrna.core.seq.tests.region_test.TestUnite method) test_two_overlapping_refseq() (seismicrna.core.seq.tests.region_test.TestUnite method) test_two_unmated_improper() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) test_two_unmated_proper() (seismicrna.relate.tests.sam_test.TestIterRecordsPaired method) test_two_valid() (seismicrna.core.seq.tests.region_test.TestGetSharedIndex method) test_type() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_unequal() (seismicrna.core.mu.tests.dim_test.TestCountsPosConsensus method) test_unmasked() (seismicrna.core.seq.tests.region_test.TestRegionUnmasked method) test_unmasked_bool() (seismicrna.core.seq.tests.region_test.TestRegionUnmasked method) test_unmasked_int() (seismicrna.core.seq.tests.region_test.TestRegionUnmasked method) test_unmasked_zero() (seismicrna.core.seq.tests.region_test.TestRegionUnmasked method) test_unpaired() (seismicrna.core.rna.tests.pair_test.TestConstants method) (seismicrna.relate.tests.relate_test.TestCalcRelsLinesPaired method) test_update_mask() (seismicrna.core.seq.tests.region_test.TestRegionAddMask method) test_update_mask_complement() (seismicrna.core.seq.tests.region_test.TestRegionAddMask method) test_valid() (seismicrna.core.batch.tests.ends_test.TestCountReadsSegments method) (seismicrna.core.batch.tests.ends_test.TestMergeReadEnds method) (seismicrna.core.seq.tests.fasta_test.TestValidFastaSeqname method) (seismicrna.core.seq.tests.xna_test.TestDNA method) (seismicrna.core.seq.tests.xna_test.TestRNA method) (seismicrna.core.tests.header_test.TestValidateKs method) test_valid_blank_line() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_valid_dna() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_valid_empty() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_valid_empty_1() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_valid_empty_seq() (seismicrna.core.seq.tests.region_test.TestIndexToSeq method) (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_valid_full() (seismicrna.core.seq.tests.region_test.TestIndexToPos method) (seismicrna.core.seq.tests.region_test.TestIndexToSeq method) test_valid_full_1() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_valid_full_9() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_valid_names() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) (seismicrna.core.seq.tests.fasta_test.TestWriteFasta method) test_valid_no_pos() (seismicrna.core.seq.tests.region_test.TestIndexToSeq method) test_valid_noncontig() (seismicrna.core.seq.tests.region_test.TestIndexToPos method) (seismicrna.core.seq.tests.region_test.TestIndexToSeq method) test_valid_noncontig_2() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_valid_rna() (seismicrna.core.seq.tests.fasta_test.TestParseFasta method) test_valid_slice() (seismicrna.core.seq.tests.region_test.TestIndexToPos method) (seismicrna.core.seq.tests.region_test.TestIndexToSeq method) test_valid_slice_6() (seismicrna.core.seq.tests.region_test.TestSeqPosToIndex method) test_verbosity() (seismicrna.core.tests.logs_test.TestSetConfig method) test_wf_sim_2samples_2refs_20000reads_2clusts() (seismicrna.tests.wf_test.TestWorkflow method) test_wf_two_out_dirs() (seismicrna.tests.wf_test.TestWorkflowTwoOutDirs method) test_whole_numbers() (seismicrna.core.tests.array_test.TestTriangular method) test_window_0() (seismicrna.core.seq.tests.region_test.TestWindowToMargins method) test_window_float() (seismicrna.core.seq.tests.region_test.TestWindowToMargins method) test_window_length() (seismicrna.core.seq.tests.region_test.TestWindowToMargins method) test_window_margins() (seismicrna.core.seq.tests.region_test.TestWindowToMargins method) test_with_clip() (seismicrna.core.tests.unbias_test.TestClip method) test_without_clip() (seismicrna.core.tests.unbias_test.TestClip method) test_wrong_dims() (seismicrna.core.batch.tests.ends_test.TestCountReadsSegments method) (seismicrna.core.batch.tests.ends_test.TestMergeReadEnds method) test_xaax_insert3() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_xaax_insert5() (seismicrna.relate.aux.tests.iterrel_test.TestIterRelvecsQ53 method) test_yes_nos() (seismicrna.core.rel.tests.pattern_test.TestRelPattern method) test_zero() (seismicrna.core.tests.header_test.TestFormatClustName method) (seismicrna.core.tests.header_test.TestFormatClustNames method) (seismicrna.core.tests.header_test.TestListClusts method) (seismicrna.core.tests.header_test.TestListKClusts method) (seismicrna.core.tests.header_test.TestListKsClusts method) (seismicrna.core.tests.header_test.TestValidateKClust method) (seismicrna.core.tests.header_test.TestValidateKs method) test_zero_degenerate() (seismicrna.core.seq.tests.xna_test.TestExpandDegenerateSeq method) test_zero_half() (seismicrna.core.mu.tests.compare_test.TestCalcArcsineDistance method) test_zero_invalid() (seismicrna.core.seq.tests.region_test.TestGetSharedIndex method) test_zero_le_gap_lt_npos() (seismicrna.core.tests.unbias_test.TestAdjustMinGap method) test_zero_length_1_to_0_keep() (seismicrna.sim.tests.ends_test.TestSimPEnds method) test_zero_length_9_to_8_drop() (seismicrna.sim.tests.ends_test.TestSimPEnds method) test_zero_length_9_to_8_keep() (seismicrna.sim.tests.ends_test.TestSimPEnds method) test_zero_lt_npos_le_gap() (seismicrna.core.tests.unbias_test.TestAdjustMinGap method) test_zero_negative() (seismicrna.core.tests.header_test.TestValidateKClust method) test_zero_one() (seismicrna.core.mu.tests.compare_test.TestCalcArcsineDistance method) test_zero_one_allowed() (seismicrna.core.tests.header_test.TestValidateKClust method) test_zero_valid() (seismicrna.core.seq.tests.region_test.TestGetSharedIndex method) TestAccumulateBatches (class in seismicrna.core.batch.tests.accum_test) TestAdjustMinGap (class in seismicrna.core.tests.unbias_test) TestAlignmentScoreParams (class in seismicrna.align.tests.xamgen_test) TestAnyNaN (class in seismicrna.core.mu.tests.nan_test) TestAssignClusterings (class in seismicrna.cluster.tests.emk_test) TestAutoReframe (class in seismicrna.core.mu.tests.frame_test) TestAutoRemoveNaN (class in seismicrna.core.mu.tests.nan_test) TestAutoRemovesNaN (class in seismicrna.core.mu.tests.nan_test) TestBootstrapJackpotScores (class in seismicrna.cluster.tests.jackpot_test) TestCalcArcsineDistance (class in seismicrna.core.mu.tests.compare_test) TestCalcBetaMV (class in seismicrna.core.tests.stats_test) TestCalcBetaParams (class in seismicrna.core.tests.stats_test) TestCalcCoeffDeterm (class in seismicrna.core.mu.tests.compare_test) TestCalcCountPerPos (class in seismicrna.core.batch.tests.count_test) TestCalcCountPerRead (class in seismicrna.core.batch.tests.count_test) TestCalcCoverage (class in seismicrna.core.batch.tests.count_test) TestCalcDirichletMV (class in seismicrna.core.tests.stats_test) TestCalcDirichletParams (class in seismicrna.core.tests.stats_test) TestCalcFlags (class in seismicrna.align.tests.write_test) TestCalcGini (class in seismicrna.core.mu.tests.measure_test) TestCalcInverse (class in seismicrna.core.tests.array_test) TestCalcMeanAbsFoldChangeOdds (class in seismicrna.core.mu.tests.compare_test) TestCalcMutsMatrix (class in seismicrna.core.batch.tests.muts_test) TestCalcParams (class in seismicrna.core.tests.unbias_test) TestCalcPClust (class in seismicrna.core.tests.unbias_test) TestCalcPClustGivenEndsNoClose (class in seismicrna.core.tests.unbias_test) TestCalcPClustGivenNoClose (class in seismicrna.core.tests.unbias_test) TestCalcPearson (class in seismicrna.core.mu.tests.compare_test) TestCalcPEnds (class in seismicrna.core.tests.unbias_test) TestCalcPEndsGivenClustNoClose (class in seismicrna.core.tests.unbias_test) TestCalcPEndsGivenNoClose (class in seismicrna.core.tests.unbias_test) TestCalcPEndsObserved (class in seismicrna.core.tests.unbias_test) TestCalcPMutGivenSpan (class in seismicrna.core.tests.unbias_test) TestCalcPMutGivenSpanNoClose (class in seismicrna.core.tests.unbias_test) TestCalcPNoClose (class in seismicrna.core.tests.unbias_test) TestCalcPNoCloseGivenClust (class in seismicrna.core.tests.unbias_test) TestCalcPNoCloseGivenEnds (class in seismicrna.core.tests.unbias_test) TestCalcPNoCloseGivenEndsAuto (class in seismicrna.core.tests.unbias_test) TestCalcPoolSize (class in seismicrna.core.tests.task_test) TestCalcQuantile (class in seismicrna.core.mu.tests.scale_test) TestCalcRanks (class in seismicrna.core.mu.tests.scale_test) TestCalcRectangularSum (class in seismicrna.core.tests.unbias_test) TestCalcRegions (class in seismicrna.tests.ensembles_test) TestCalcRelsLinesPaired (class in seismicrna.relate.tests.relate_test) TestCalcRelsLinesSingle (class in seismicrna.relate.tests.relate_test) TestCalcRelsPerPos (class in seismicrna.core.batch.tests.count_test) TestCalcRelsPerRead (class in seismicrna.core.batch.tests.count_test) TestCalcSemiGAnomaly (class in seismicrna.cluster.tests.jackpot_test) TestCalcSignalNoise (class in seismicrna.core.mu.tests.measure_test) TestCalcSpearman (class in seismicrna.core.mu.tests.compare_test) TestCalcSumAbsDiffLogOdds (class in seismicrna.core.mu.tests.compare_test) TestCalcUniqReadWeights (class in seismicrna.core.batch.tests.count_test) TestCheckNoCoverageReads (class in seismicrna.core.batch.tests.ends_test) TestCigarOp (class in seismicrna.relate.aux.tests.cigarop_test) TestClip (class in seismicrna.core.tests.unbias_test) TestClustHeader (class in seismicrna.core.tests.header_test) TestCompareWindows (class in seismicrna.core.mu.tests.compare_test) TestConsistentVersion (class in seismicrna.core.tests.version_test) TestConstants (class in seismicrna.core.ngs.tests.phred_test) (class in seismicrna.core.rel.tests.code_test) (class in seismicrna.core.rna.tests.pair_test) (class in seismicrna.core.seq.tests.region_test) (class in seismicrna.core.tests.header_test) TestCountCigarMuts (class in seismicrna.relate.aux.tests.cigarop_test) TestCountEndCoords (class in seismicrna.core.batch.tests.count_test) TestCountPos (class in seismicrna.core.mu.tests.dim_test) TestCountReadsSegments (class in seismicrna.core.batch.tests.ends_test) TestCountsPos (class in seismicrna.core.mu.tests.dim_test) TestCountsPosConsensus (class in seismicrna.core.mu.tests.dim_test) TestDecode (class in seismicrna.core.ngs.tests.phred_test) TestDeduplicateRels (class in seismicrna.core.tests.header_test) TestDictToPairs (class in seismicrna.core.rna.tests.pair_test) TestDictToTable (class in seismicrna.core.rna.tests.pair_test) TestDNA (class in seismicrna.core.seq.tests.xna_test) TestEncode (class in seismicrna.core.ngs.tests.phred_test) TestEncodeRelate (class in seismicrna.relate.py.tests.encode_test) TestEnsembles (class in seismicrna.tests.ensembles_test) TestEnsureSameLength (class in seismicrna.core.tests.array_test) TestEqualHeaders (class in seismicrna.core.tests.header_test) TestEraseConfig (class in seismicrna.core.tests.logs_test) TestExcInfo (class in seismicrna.core.tests.logs_test) TestExpandDegenerateSeq (class in seismicrna.core.seq.tests.xna_test) TestFindCigarOpPosRead (class in seismicrna.relate.aux.tests.cigarop_test) TestFindContiguousReads (class in seismicrna.core.batch.tests.ends_test) TestFindDims (class in seismicrna.core.tests.array_test) TestFindEnclosingPairs (class in seismicrna.core.rna.tests.pair_test) TestFindReadEnd3s (class in seismicrna.core.batch.tests.ends_test) TestFindReadEnd5s (class in seismicrna.core.batch.tests.ends_test) TestFindSplitPositions (class in seismicrna.core.tests.unbias_test) TestFlagsCmds (class in seismicrna.align.tests.xamops_test) TestFormat (class in seismicrna.core.seq.tests.fasta_test) TestFormatClustName (class in seismicrna.core.tests.header_test) TestFormatClustNames (class in seismicrna.core.tests.header_test) TestFormatDbStructure (class in seismicrna.core.rna.tests.db_test) TestFormatVersion (class in seismicrna.core.tests.version_test) TestGetComp (class in seismicrna.core.mu.tests.compare_test) TestGetConfig (class in seismicrna.core.tests.logs_test) TestGetLength (class in seismicrna.core.tests.array_test) TestGetSeismicRNASourceDir (class in seismicrna.core.tests.path_test) TestGetSharedIndex (class in seismicrna.core.seq.tests.region_test) TestGetWindows (class in seismicrna.core.seq.tests.region_test) TestHalfRelPattern (class in seismicrna.core.rel.tests.pattern_test) TestHeader (class in seismicrna.core.tests.header_test) TestHyphenateEnds (class in seismicrna.core.seq.tests.region_test) TestIndexToPos (class in seismicrna.core.seq.tests.region_test) TestIndexToSeq (class in seismicrna.core.seq.tests.region_test) TestInferRead (class in seismicrna.relate.aux.tests.infer_test) TestIntersect (class in seismicrna.core.seq.tests.region_test) TestIsACGT (class in seismicrna.relate.py.tests.encode_test) TestIterRecordsPaired (class in seismicrna.relate.tests.sam_test) TestIterRelvecsAll (class in seismicrna.relate.aux.tests.iterrel_test) TestIterRelvecsQ53 (class in seismicrna.relate.aux.tests.iterrel_test) TestLevels (class in seismicrna.core.tests.logs_test) TestLineAttrs (class in seismicrna.relate.tests.sam_test) TestListClusts (class in seismicrna.core.tests.header_test) TestListKClusts (class in seismicrna.core.tests.header_test) TestListKsClusts (class in seismicrna.core.tests.header_test) TestLocateElements (class in seismicrna.core.tests.array_test) TestLoggerClass (class in seismicrna.core.tests.logs_test) TestLoggingRaiseOnError (class in seismicrna.core.tests.logs_test) TestMakeHeader (class in seismicrna.core.tests.header_test) TestMarginalResps (class in seismicrna.cluster.tests.marginal_test) TestMask (class in seismicrna.mask.tests.main_test) TestMask1Batch (class in seismicrna.mask.tests.main_test) TestMask1Sample (class in seismicrna.mask.tests.main_test) TestMask2Samples (class in seismicrna.mask.tests.main_test) TestMaskBatches (class in seismicrna.mask.tests.main_test) TestMaskPaired (class in seismicrna.mask.tests.main_test) TestMaskSegmentEnds (class in seismicrna.core.batch.tests.ends_test) TestMaskSingle (class in seismicrna.mask.tests.main_test) TestMaskSingle1Sample1Batch (class in seismicrna.mask.tests.main_test) TestMatchReadsSegments (class in seismicrna.core.batch.tests.ends_test) TestMergeMates (class in seismicrna.relate.tests.relate_test) TestMergeReadEnds (class in seismicrna.core.batch.tests.ends_test) TestMergeSegmentEnds (class in seismicrna.core.batch.tests.ends_test) TestNoCloseMuts (class in seismicrna.core.tests.unbias_test) TestNoNaN (class in seismicrna.core.mu.tests.nan_test) TestNormalize (class in seismicrna.core.mu.tests.scale_test) (class in seismicrna.core.tests.unbias_test) TestPairedMarks (class in seismicrna.core.rna.tests.db_test) TestPairsToDict (class in seismicrna.core.rna.tests.pair_test) TestPairsToTable (class in seismicrna.core.rna.tests.pair_test) TestParseCigar (class in seismicrna.relate.py.tests.cigar_test) TestParseDbStructure (class in seismicrna.core.rna.tests.db_test) TestParseFasta (class in seismicrna.core.seq.tests.fasta_test) TestParseHeader (class in seismicrna.core.tests.header_test) TestParseVersion (class in seismicrna.core.tests.version_test) TestQuickUnbias (class in seismicrna.core.tests.unbias_test) TestReframe (class in seismicrna.core.mu.tests.frame_test) TestReframeLike (class in seismicrna.core.mu.tests.frame_test) TestRegionAddMask (class in seismicrna.core.seq.tests.region_test) TestRegionCopy (class in seismicrna.core.seq.tests.region_test) TestRegionEqual (class in seismicrna.core.seq.tests.region_test) TestRegionInit (class in seismicrna.core.seq.tests.region_test) TestRegionLength (class in seismicrna.core.seq.tests.region_test) TestRegionMasked (class in seismicrna.core.seq.tests.region_test) TestRegionMaskGU (class in seismicrna.core.seq.tests.region_test) TestRegionMaskList (class in seismicrna.core.seq.tests.region_test) TestRegionMaskNames (class in seismicrna.core.seq.tests.region_test) TestRegionMaskPolyA (class in seismicrna.core.seq.tests.region_test) TestRegionRange (class in seismicrna.core.seq.tests.region_test) TestRegionUnmasked (class in seismicrna.core.seq.tests.region_test) TestRelate (class in seismicrna.relate.tests.main_test) TestRelateEmpty (class in seismicrna.relate.tests.main_test) TestRelatePaired (class in seismicrna.relate.tests.main_test) TestRelateSingle (class in seismicrna.relate.tests.main_test) TestRelClustHeader (class in seismicrna.core.tests.header_test) TestRelHeader (class in seismicrna.core.tests.header_test) TestRelPattern (class in seismicrna.core.rel.tests.pattern_test) TestRemoveNaNs (class in seismicrna.core.mu.tests.nan_test) TestRemovesNaNs (class in seismicrna.core.mu.tests.nan_test) TestRestoreConfig (class in seismicrna.core.tests.logs_test) TestRNA (class in seismicrna.core.seq.tests.xna_test) TestSeqPosToIndex (class in seismicrna.core.seq.tests.region_test) TestSetConfig (class in seismicrna.core.tests.logs_test) TestSimClusters (class in seismicrna.cluster.tests.jackpot_test) TestSimPEnds (class in seismicrna.sim.tests.ends_test) TestSimReads (class in seismicrna.cluster.tests.jackpot_test) TestSlicePEnds (class in seismicrna.core.tests.unbias_test) TestSortSegmentEnds (class in seismicrna.core.batch.tests.ends_test) TestStochasticRound (class in seismicrna.core.tests.random_test) TestSubregion (class in seismicrna.core.seq.tests.region_test) TestSubsCoding (class in seismicrna.relate.py.tests.encode_test) TestSymlinkIfNeeded (class in seismicrna.core.tests.path_test) TestTableToDict (class in seismicrna.core.rna.tests.pair_test) TestTableToPairs (class in seismicrna.core.rna.tests.pair_test) TestTriangular (class in seismicrna.core.tests.array_test) TestTriuAllClose (class in seismicrna.core.tests.unbias_test) TestTriuCumSum (class in seismicrna.core.tests.unbias_test) TestTriuDiv (class in seismicrna.core.tests.unbias_test) TestTriuDot (class in seismicrna.core.tests.unbias_test) TestTriuLog (class in seismicrna.core.tests.unbias_test) TestTriuMul (class in seismicrna.core.tests.unbias_test) TestTriuNorm (class in seismicrna.core.tests.unbias_test) TestTriuSum (class in seismicrna.core.tests.unbias_test) TestUnite (class in seismicrna.core.seq.tests.region_test) TestValidateKClust (class in seismicrna.core.tests.header_test) TestValidateKs (class in seismicrna.core.tests.header_test) TestValidFastaSeqname (class in seismicrna.core.seq.tests.fasta_test) TestWindowToMargins (class in seismicrna.core.seq.tests.region_test) TestWinsorize (class in seismicrna.core.mu.tests.scale_test) TestWorkflow (class in seismicrna.tests.wf_test) TestWorkflowTwoOutDirs (class in seismicrna.tests.wf_test) TestWriteFasta (class in seismicrna.core.seq.tests.fasta_test) TestXNA (class in seismicrna.core.seq.tests.xna_test) timestamp (seismicrna.core.dataset.Dataset property) (seismicrna.core.dataset.LoadedDataset property) (seismicrna.core.dataset.MergedDataset property) (seismicrna.core.dataset.MultistepDataset property) title (seismicrna.core.report.Field attribute) (seismicrna.core.report.OptionField attribute) (seismicrna.graph.base.BaseGraph property) title_action_sample (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.graph.onesource.OneSourceGraph property) (seismicrna.graph.twotable.TwoTableGraph property) TMP_PFX (seismicrna.align.tests.xamops_test.TestFlagsCmds attribute) tmp_sam_path (seismicrna.relate.sam.XamViewer property) tmp_xam_cmd() (in module seismicrna.relate.sam) to_ct() (in module seismicrna.core.rna.io) to_db() (in module seismicrna.core.rna.io) to_dict() (seismicrna.core.report.Report method) (seismicrna.core.seq.region.Region method) (seismicrna.draw.draw.ColorBlock method) (seismicrna.draw.draw.JinjaData method) to_dms() (seismicrna.core.rna.profile.RNAProfile method) to_fasta() (seismicrna.core.rna.profile.RNAProfile method) to_new() (seismicrna.align.fqunit.FastqUnit method) to_report_format() (seismicrna.core.rel.pattern.HalfRelPattern method) to_varna_color_file() (seismicrna.core.rna.profile.RNAProfile method) top (seismicrna.core.dataset.Dataset property) (seismicrna.core.table.base.Table property) (seismicrna.core.table.write.TableWriter property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.dataset.DatasetGraph property) (seismicrna.graph.onetable.OneTableGraph property) (seismicrna.graph.twotable.TwoTableGraph property) (seismicrna.relate.table.TableLoader property) tpr (seismicrna.graph.roc.ROCGraph property) tr() (seismicrna.core.seq.xna.DNA method) transpath() (in module seismicrna.core.path) transpaths() (in module seismicrna.core.path) triangular() (in module seismicrna.core.array) triu_allclose() (in module seismicrna.core.unbias) triu_dot() (in module seismicrna.core.unbias) triu_log() (in module seismicrna.core.unbias) triu_sum() (in module seismicrna.core.unbias) try_move() (seismicrna.relate.py.ambindel.Deletion method) (seismicrna.relate.py.ambindel.Indel method) (seismicrna.relate.py.ambindel.Insertion method) TwoTableGraph (class in seismicrna.graph.twotable) TwoTableMergedClusterGroupGraph (class in seismicrna.graph.twotable) TwoTableRelClusterGroupGraph (class in seismicrna.graph.twotable) TwoTableRelClusterGroupRunner (class in seismicrna.graph.twotable) TwoTableRelClusterGroupWriter (class in seismicrna.graph.twotable) TwoTableRunner (class in seismicrna.graph.twotable) TwoTableWriter (class in seismicrna.graph.twotable) type (seismicrna.core.seq.xna.CompressedSeq property)

U

UnbiasDataset (class in seismicrna.core.dataset) uniq_names (seismicrna.cluster.uniq.UniqReads property) UniqReads (class in seismicrna.cluster.uniq) unite() (in module seismicrna.core.seq.region) universal_input_params() (seismicrna.graph.base.BaseRunner class method)

universal_output_params() (seismicrna.graph.base.BaseRunner class method) unmasked (seismicrna.core.seq.region.Region property) unmasked_bool (seismicrna.core.seq.region.Region property) unmasked_int (seismicrna.core.seq.region.Region property) unmasked_zero (seismicrna.core.seq.region.Region property)

V

valid_fasta_seqname() (in module seismicrna.core.seq.fasta) validate() (seismicrna.core.path.Field method) validate_int() (in module seismicrna.core.path) validate_k_clust() (in module seismicrna.core.header) validate_ks() (in module seismicrna.core.header) validate_str() (in module seismicrna.core.path) validate_top() (in module seismicrna.core.path) var_params() (seismicrna.graph.base.BaseRunner class method) (seismicrna.graph.cgroup.ClusterGroupRunner class method) (seismicrna.graph.corroll.RollingCorrelationRunner class method) (seismicrna.graph.dataset.DatasetRunner class method) (seismicrna.graph.hist.HistogramRunner class method) (seismicrna.graph.mutdist.MutationDistanceRunner class method) (seismicrna.graph.onestruct.StructOneTableRunner class method) (seismicrna.graph.rel.RelRunner class method) (seismicrna.graph.roll.RollingRunner class method) (seismicrna.graph.scatter.ScatterRunner class method) (seismicrna.graph.table.RelTableRunner class method) (seismicrna.graph.table.TableRunner class method) (seismicrna.graph.twotable.TwoTableRunner class method)

verbosity (seismicrna.core.logs.Filterer attribute) (seismicrna.core.logs.LoggerConfig attribute) verify_index_names() (in module seismicrna.core.seq.region) verify_proportions() (in module seismicrna.sim.muts) view_xam_cmd() (in module seismicrna.core.ngs.xam)

W

WARNING (seismicrna.core.logs.Level attribute) warning() (seismicrna.core.logs.Logger method) what() (seismicrna.graph.abundance.ClusterAbundanceGraph class method) (seismicrna.graph.aucroll.RollingAUCGraph class method) (seismicrna.graph.base.BaseGraph class method) (seismicrna.graph.corroll.RollingCorrelationGraph class method) (seismicrna.graph.delprof.DeltaProfileGraph class method) (seismicrna.graph.giniroll.RollingGiniGraph class method) (seismicrna.graph.histpos.PositionHistogramGraph class method) (seismicrna.graph.histread.ReadHistogramGraph class method) (seismicrna.graph.mutdist.MutationDistanceGraph class method) (seismicrna.graph.poscorr.PositionCorrelationGraph class method) (seismicrna.graph.profile.MultiRelsProfileGraph class method) (seismicrna.graph.profile.OneRelProfileGraph class method) (seismicrna.graph.roc.ROCGraph class method) (seismicrna.graph.scatter.ScatterGraph class method) (seismicrna.graph.snrroll.RollingSNRGraph class method) WideDataset (class in seismicrna.core.dataset) WideMutsDataset (class in seismicrna.core.dataset) window_to_margins() (in module seismicrna.core.seq.region) winsorize() (in module seismicrna.core.mu.scale) with_tmp_dir() (in module seismicrna.core.tmp) write() (seismicrna.core.table.write.TableWriter method) (seismicrna.graph.base.BaseGraph method) (seismicrna.graph.base.BaseWriter method) (seismicrna.relate.write.RelationWriter method)

write_batches() (seismicrna.cluster.io.ClusterBatchWriter method) write_both_strands() (in module seismicrna.relate.strands) write_csv() (seismicrna.graph.base.BaseGraph method) write_datasets() (in module seismicrna.mask.tests.main_test) write_fasta() (in module seismicrna.core.seq.fasta) write_fasta_file() (in module seismicrna.relate.tests.main_test) write_html() (seismicrna.graph.base.BaseGraph method) write_mode() (in module seismicrna.core.write) write_mus() (in module seismicrna.cluster.params) write_obs_exp_counts() (in module seismicrna.cluster.obsexp) write_pdf() (seismicrna.graph.base.BaseGraph method) write_pis() (in module seismicrna.cluster.params) write_png() (seismicrna.graph.base.BaseGraph method) write_report() (in module seismicrna.join) (in module seismicrna.pool) write_sam() (in module seismicrna.relate.tests.sam_test) write_sam_file() (in module seismicrna.relate.tests.main_test) write_single_run_table() (in module seismicrna.cluster.params) write_summaries() (in module seismicrna.cluster.summary) write_svg() (seismicrna.graph.base.BaseGraph method) write_table() (in module seismicrna.cluster.summary) write_tables() (seismicrna.core.table.write.Tabulator method) write_tmp_ref_files() (in module seismicrna.align.write) WrongChecksumError WrongFileExtensionError

X

x_title (seismicrna.graph.abundance.ClusterAbundanceGraph property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.delprof.DeltaProfileGraph property) (seismicrna.graph.hist.HistogramGraph property) (seismicrna.graph.mutdist.MutationDistanceGraph property) (seismicrna.graph.pospair.PositionPairGraph property) (seismicrna.graph.profile.ProfileGraph property) (seismicrna.graph.roc.ROCGraph property) (seismicrna.graph.roll.RollingGraph property) (seismicrna.graph.scatter.ScatterGraph property)

XAM_INP (seismicrna.align.tests.xamops_test.TestFlagsCmds attribute) XAM_OUT (seismicrna.align.tests.xamops_test.TestFlagsCmds attribute) xam_paired() (in module seismicrna.core.ngs.xam) xam_to_fastq_cmd() (in module seismicrna.core.ngs.xam) xamgen_cmd() (in module seismicrna.align.xamops) XamViewer (class in seismicrna.relate.sam) xmax (seismicrna.graph.scatter.ScatterGraph property) XNA (class in seismicrna.core.seq.xna)

Y

y_title (seismicrna.graph.abundance.ClusterAbundanceGraph property) (seismicrna.graph.aucroll.RollingAUCGraph property) (seismicrna.graph.base.BaseGraph property) (seismicrna.graph.corroll.RollingCorrelationGraph property) (seismicrna.graph.delprof.DeltaProfileGraph property) (seismicrna.graph.giniroll.RollingGiniGraph property) (seismicrna.graph.histpos.PositionHistogramGraph property) (seismicrna.graph.histread.ReadHistogramGraph property) (seismicrna.graph.mutdist.MutationDistanceGraph property) (seismicrna.graph.pospair.PositionPairGraph property) (seismicrna.graph.profile.ProfileGraph property) (seismicrna.graph.roc.ROCGraph property) (seismicrna.graph.scatter.ScatterGraph property) (seismicrna.graph.snrroll.RollingSNRGraph property)

yes (seismicrna.core.rel.pattern.RelPattern attribute) ymax (seismicrna.graph.scatter.ScatterGraph property)