Index

Symbols

--add-columns pairtools-parse command line option pairtools-parse2 command line option --add-pair-index pairtools-parse command line option pairtools-parse2 command line option --assembly pairtools-header-generate command line option pairtools-parse command line option pairtools-parse2 command line option --backend pairtools-dedup command line option --bytile-dups pairtools-stats command line option --c1 pairtools-dedup command line option pairtools-filterbycov command line option pairtools-sort command line option --c2 pairtools-dedup command line option pairtools-filterbycov command line option pairtools-sort command line option --carryover pairtools-dedup command line option --chrom-subset pairtools-dedup command line option pairtools-select command line option pairtools-stats command line option --chroms-path pairtools-flip command line option pairtools-header-generate command line option pairtools-parse command line option pairtools-parse2 command line option --chunksize pairtools-dedup command line option pairtools-scaling command line option --clean-output pairtools-phase command line option --cmd-in pairtools-dedup command line option pairtools-filterbycov command line option pairtools-flip command line option pairtools-header-generate command line option pairtools-header-set-columns command line option pairtools-header-transfer command line option pairtools-header-validate-columns command line option pairtools-markasdup command line option pairtools-merge command line option pairtools-parse command line option pairtools-parse2 command line option pairtools-phase command line option pairtools-restrict command line option pairtools-sample command line option pairtools-scaling command line option pairtools-select command line option pairtools-sort command line option pairtools-split command line option pairtools-stats command line option --cmd-out pairtools-dedup command line option pairtools-filterbycov command line option pairtools-flip command line option pairtools-header-generate command line option pairtools-header-set-columns command line option pairtools-header-transfer command line option pairtools-header-validate-columns command line option pairtools-markasdup command line option pairtools-merge command line option pairtools-parse command line option pairtools-parse2 command line option pairtools-phase command line option pairtools-restrict command line option pairtools-sample command line option pairtools-scaling command line option pairtools-select command line option pairtools-sort command line option pairtools-split command line option pairtools-stats command line option --columns pairtools-header-generate command line option pairtools-header-set-columns command line option --comment-char pairtools-filterbycov command line option --compress-program pairtools-merge command line option pairtools-sort command line option --concatenate pairtools-merge command line option --debug pairtools command line option --dedup-max-mismatch pairtools-parse2 command line option --dist-range pairtools-scaling command line option --drop-readid pairtools-parse command line option pairtools-parse2 command line option --drop-sam pairtools-parse command line option pairtools-parse2 command line option --drop-seq pairtools-parse command line option pairtools-parse2 command line option --engine pairtools-dedup command line option pairtools-stats command line option --expand pairtools-parse2 command line option --extra-col pairtools-sort command line option --extra-col-pair pairtools-dedup command line option --extra-columns pairtools-header-generate command line option --filter pairtools-dedup command line option pairtools-stats command line option --flip pairtools-parse command line option pairtools-parse2 command line option --frags pairtools-restrict command line option --keep-first-header pairtools-merge command line option --keep-parent-id pairtools-dedup command line option --keep-readid pairtools-parse2 command line option --keep-sam pairtools-parse2 command line option --keep-seq pairtools-parse2 command line option --mark-dups pairtools-dedup command line option --mark-multi pairtools-filterbycov command line option --max-cov pairtools-filterbycov command line option --max-dist pairtools-filterbycov command line option --max-expansion-depth pairtools-parse2 command line option --max-insert-size pairtools-parse2 command line option --max-inter-align-gap pairtools-parse command line option pairtools-parse2 command line option --max-mismatch pairtools-dedup command line option --max-molecule-size pairtools-parse command line option --max-nmerge pairtools-merge command line option --memory pairtools-merge command line option pairtools-sort command line option --merge pairtools-stats command line option --method pairtools-dedup command line option pairtools-filterbycov command line option --min-mapq pairtools-parse command line option pairtools-parse2 command line option --n-dist-bins-decade pairtools-scaling command line option pairtools-stats command line option --n-proc pairtools-dedup command line option --no-bytile-dups pairtools-stats command line option --no-chromsizes pairtools-stats command line option --no-concatenate pairtools-merge command line option --no-expand pairtools-parse2 command line option --no-flip pairtools-header-generate command line option pairtools-parse command line option pairtools-parse2 command line option --no-keep-first-header pairtools-merge command line option --no-mark-dups pairtools-dedup command line option --no-report-scores pairtools-phase command line option --no-yaml pairtools-dedup command line option pairtools-stats command line option --nproc pairtools-merge command line option pairtools-sort command line option --nproc-in pairtools-dedup command line option pairtools-filterbycov command line option pairtools-flip command line option pairtools-header-generate command line option pairtools-header-set-columns command line option pairtools-header-transfer command line option pairtools-header-validate-columns command line option pairtools-markasdup command line option pairtools-merge command line option pairtools-parse command line option pairtools-parse2 command line option pairtools-phase command line option pairtools-restrict command line option pairtools-sample command line option pairtools-scaling command line option pairtools-select command line option pairtools-sort command line option pairtools-split command line option pairtools-stats command line option

--nproc-out pairtools-dedup command line option pairtools-filterbycov command line option pairtools-flip command line option pairtools-header-generate command line option pairtools-header-set-columns command line option pairtools-header-transfer command line option pairtools-header-validate-columns command line option pairtools-markasdup command line option pairtools-merge command line option pairtools-parse command line option pairtools-parse2 command line option pairtools-phase command line option pairtools-restrict command line option pairtools-sample command line option pairtools-scaling command line option pairtools-select command line option pairtools-sort command line option pairtools-split command line option pairtools-stats command line option --output pairtools-dedup command line option pairtools-filterbycov command line option pairtools-flip command line option pairtools-header-generate command line option pairtools-header-set-columns command line option pairtools-header-transfer command line option pairtools-header-validate-columns command line option pairtools-markasdup command line option pairtools-merge command line option pairtools-parse command line option pairtools-parse2 command line option pairtools-phase command line option pairtools-restrict command line option pairtools-sample command line option pairtools-scaling command line option pairtools-select command line option pairtools-sort command line option pairtools-stats command line option --output-bytile-stats pairtools-dedup command line option pairtools-stats command line option --output-dups pairtools-dedup command line option --output-highcov pairtools-filterbycov command line option --output-pairs pairtools-split command line option --output-parsed-alignments pairtools-parse command line option pairtools-parse2 command line option --output-profile pairtools command line option --output-rest pairtools-select command line option --output-sam pairtools-split command line option --output-stats pairtools-dedup command line option pairtools-filterbycov command line option pairtools-parse command line option pairtools-parse2 command line option --output-unmapped pairtools-dedup command line option pairtools-filterbycov command line option --p1 pairtools-dedup command line option pairtools-filterbycov command line option pairtools-sort command line option --p2 pairtools-dedup command line option pairtools-filterbycov command line option pairtools-sort command line option --pairs pairtools-header-generate command line option --pairsam pairtools-header-generate command line option --phase-suffixes pairtools-phase command line option --post-mortem pairtools command line option --pt pairtools-sort command line option --readid-transform pairtools-parse command line option pairtools-parse2 command line option --reference-columns pairtools-header-validate-columns command line option --reference-file pairtools-header-transfer command line option pairtools-header-validate-columns command line option --regions pairtools-scaling command line option --remove-columns pairtools-select command line option --report-alignment-end pairtools-parse command line option --report-orientation pairtools-parse2 command line option --report-position pairtools-parse2 command line option --report-scores pairtools-phase command line option --s1 pairtools-dedup command line option pairtools-filterbycov command line option --s2 pairtools-dedup command line option pairtools-filterbycov command line option --sam-path pairtools-header-generate command line option --seed pairtools-sample command line option --send-header-to pairtools-dedup command line option pairtools-filterbycov command line option --sep pairtools-dedup command line option pairtools-filterbycov command line option --single-end pairtools-parse2 command line option --startup-code pairtools-dedup command line option pairtools-select command line option pairtools-stats command line option --tag-mode pairtools-phase command line option --tmpdir pairtools-merge command line option pairtools-sort command line option --type-cast pairtools-dedup command line option pairtools-select command line option pairtools-stats command line option --unmapped-chrom pairtools-dedup command line option pairtools-filterbycov command line option --verbose pairtools command line option --version pairtools command line option --view pairtools-scaling command line option --walks-policy pairtools-parse command line option --with-chromsizes pairtools-stats command line option --yaml pairtools-dedup command line option pairtools-stats command line option -c pairtools-flip command line option pairtools-header-set-columns command line option pairtools-header-validate-columns command line option pairtools-parse command line option pairtools-parse2 command line option -d pairtools command line option -f pairtools-restrict command line option -o pairtools-dedup command line option pairtools-filterbycov command line option pairtools-flip command line option pairtools-header-generate command line option pairtools-header-set-columns command line option pairtools-header-transfer command line option pairtools-header-validate-columns command line option pairtools-markasdup command line option pairtools-merge command line option pairtools-parse command line option pairtools-parse2 command line option pairtools-phase command line option pairtools-restrict command line option pairtools-sample command line option pairtools-scaling command line option pairtools-select command line option pairtools-sort command line option pairtools-stats command line option -p pairtools-dedup command line option -r pairtools-header-transfer command line option pairtools-header-validate-columns command line option pairtools-select command line option -s pairtools-sample command line option -t pairtools-dedup command line option pairtools-select command line option pairtools-stats command line option -v pairtools command line option

C

CONDITION pairtools-select command line option

F

FRACTION pairtools-sample command line option

I

INPUT_PATH pairtools-scaling command line option pairtools-stats command line option

P

PAIRS_PATH pairtools-dedup command line option pairtools-filterbycov command line option pairtools-flip command line option pairtools-header-generate command line option pairtools-header-set-columns command line option pairtools-header-transfer command line option pairtools-header-validate-columns command line option pairtools-merge command line option pairtools-phase command line option pairtools-restrict command line option pairtools-sample command line option pairtools-select command line option pairtools-sort command line option PAIRSAM_PATH pairtools-markasdup command line option pairtools-split command line option pairtools command line option --debug --output-profile --post-mortem --verbose --version -d -v pairtools-dedup command line option --backend --c1 --c2 --carryover --chrom-subset --chunksize --cmd-in --cmd-out --engine --extra-col-pair --filter --keep-parent-id --mark-dups --max-mismatch --method --n-proc --no-mark-dups --no-yaml --nproc-in --nproc-out --output --output-bytile-stats --output-dups --output-stats --output-unmapped --p1 --p2 --s1 --s2 --send-header-to --sep --startup-code --type-cast --unmapped-chrom --yaml -o -p -t PAIRS_PATH pairtools-filterbycov command line option --c1 --c2 --cmd-in --cmd-out --comment-char --mark-multi --max-cov --max-dist --method --nproc-in --nproc-out --output --output-highcov --output-stats --output-unmapped --p1 --p2 --s1 --s2 --send-header-to --sep --unmapped-chrom -o PAIRS_PATH pairtools-flip command line option --chroms-path --cmd-in --cmd-out --nproc-in --nproc-out --output -c -o PAIRS_PATH pairtools-header-generate command line option --assembly --chroms-path --cmd-in --cmd-out --columns --extra-columns --no-flip --nproc-in --nproc-out --output --pairs --pairsam --sam-path -o PAIRS_PATH pairtools-header-set-columns command line option --cmd-in --cmd-out --columns --nproc-in --nproc-out --output -c -o PAIRS_PATH pairtools-header-transfer command line option --cmd-in --cmd-out --nproc-in --nproc-out --output --reference-file -o -r PAIRS_PATH pairtools-header-validate-columns command line option --cmd-in --cmd-out --nproc-in --nproc-out --output --reference-columns --reference-file -c -o -r PAIRS_PATH pairtools-markasdup command line option --cmd-in --cmd-out --nproc-in --nproc-out --output -o PAIRSAM_PATH pairtools-merge command line option --cmd-in --cmd-out --compress-program --concatenate --keep-first-header --max-nmerge --memory --no-concatenate --no-keep-first-header --nproc --nproc-in --nproc-out --output --tmpdir -o PAIRS_PATH

pairtools-parse command line option --add-columns --add-pair-index --assembly --chroms-path --cmd-in --cmd-out --drop-readid --drop-sam --drop-seq --flip --max-inter-align-gap --max-molecule-size --min-mapq --no-flip --nproc-in --nproc-out --output --output-parsed-alignments --output-stats --readid-transform --report-alignment-end --walks-policy -c -o SAM_PATH pairtools-parse2 command line option --add-columns --add-pair-index --assembly --chroms-path --cmd-in --cmd-out --dedup-max-mismatch --drop-readid --drop-sam --drop-seq --expand --flip --keep-readid --keep-sam --keep-seq --max-expansion-depth --max-insert-size --max-inter-align-gap --min-mapq --no-expand --no-flip --nproc-in --nproc-out --output --output-parsed-alignments --output-stats --readid-transform --report-orientation --report-position --single-end -c -o SAM_PATH pairtools-phase command line option --clean-output --cmd-in --cmd-out --no-report-scores --nproc-in --nproc-out --output --phase-suffixes --report-scores --tag-mode -o PAIRS_PATH pairtools-restrict command line option --cmd-in --cmd-out --frags --nproc-in --nproc-out --output -f -o PAIRS_PATH pairtools-sample command line option --cmd-in --cmd-out --nproc-in --nproc-out --output --seed -o -s FRACTION PAIRS_PATH pairtools-scaling command line option --chunksize --cmd-in --cmd-out --dist-range --n-dist-bins-decade --nproc-in --nproc-out --output --regions --view -o INPUT_PATH pairtools-select command line option --chrom-subset --cmd-in --cmd-out --nproc-in --nproc-out --output --output-rest --remove-columns --startup-code --type-cast -o -r -t CONDITION PAIRS_PATH pairtools-sort command line option --c1 --c2 --cmd-in --cmd-out --compress-program --extra-col --memory --nproc --nproc-in --nproc-out --output --p1 --p2 --pt --tmpdir -o PAIRS_PATH pairtools-split command line option --cmd-in --cmd-out --nproc-in --nproc-out --output-pairs --output-sam PAIRSAM_PATH pairtools-stats command line option --bytile-dups --chrom-subset --cmd-in --cmd-out --engine --filter --merge --n-dist-bins-decade --no-bytile-dups --no-chromsizes --no-yaml --nproc-in --nproc-out --output --output-bytile-stats --startup-code --type-cast --with-chromsizes --yaml -o -t INPUT_PATH

S

SAM_PATH pairtools-parse command line option pairtools-parse2 command line option