Index

Symbols

--add-columns <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 <assembly> pairtools-header-generate command line option pairtools-parse command line option pairtools-parse2 command line option --backend <backend> pairtools-dedup command line option --bytile-dups, --no-bytile-dups pairtools-stats command line option --c1 <c1> pairtools-dedup command line option pairtools-filterbycov command line option --c2 <c2> pairtools-dedup command line option pairtools-filterbycov command line option --carryover <carryover> pairtools-dedup command line option --chrom-subset <chrom_subset> pairtools-dedup command line option pairtools-select command line option pairtools-stats command line option --chroms-path <chroms_path> pairtools-header-generate command line option --chunksize <chunksize> pairtools-dedup command line option pairtools-scaling command line option --clean-output pairtools-phase command line option --cmd-in <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 <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 <columns> pairtools-header-generate command line option --comment-char <comment_char> pairtools-filterbycov command line option --compress-program <compress_program> pairtools-merge command line option pairtools-sort command line option --concatenate, --no-concatenate pairtools-merge command line option --dedup-max-mismatch <dedup_max_mismatch> pairtools-parse2 command line option --dist-range <dist_range> pairtools-scaling command line option --drop-readid pairtools-parse command line option --drop-readid, --keep-readid pairtools-parse2 command line option --drop-sam pairtools-parse command line option --drop-sam, --keep-sam pairtools-parse2 command line option --drop-seq pairtools-parse command line option --drop-seq, --keep-seq pairtools-parse2 command line option --engine <engine> pairtools-dedup command line option pairtools-stats command line option --expand, --no-expand pairtools-parse2 command line option --extra-col-pair <extra_col_pair> pairtools-dedup command line option --extra-columns <extra_columns> pairtools-header-generate command line option --filter <filter> pairtools-dedup command line option pairtools-stats command line option --flip, --no-flip pairtools-parse command line option pairtools-parse2 command line option --keep-first-header, --no-keep-first-header pairtools-merge command line option --keep-parent-id pairtools-dedup command line option --mark-dups pairtools-dedup command line option --mark-multi pairtools-filterbycov command line option --max-cov <max_cov> pairtools-filterbycov command line option --max-dist <max_dist> pairtools-filterbycov command line option --max-expansion-depth <max_expansion_depth> pairtools-parse2 command line option --max-insert-size <max_insert_size> pairtools-parse2 command line option --max-inter-align-gap <max_inter_align_gap> pairtools-parse command line option pairtools-parse2 command line option --max-mismatch <max_mismatch> pairtools-dedup command line option --max-molecule-size <max_molecule_size> pairtools-parse command line option --max-nmerge <max_nmerge> pairtools-merge command line option --memory <memory> pairtools-merge command line option pairtools-sort command line option --merge pairtools-stats command line option --method <method> pairtools-dedup command line option pairtools-filterbycov command line option --min-mapq <min_mapq> pairtools-parse command line option pairtools-parse2 command line option --n-dist-bins <n_dist_bins> pairtools-scaling command line option --no-flip pairtools-header-generate command line option --nproc <nproc> pairtools-merge command line option pairtools-sort command line option --nproc-in <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 <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-bytile-stats <output_bytile_stats> pairtools-dedup command line option pairtools-stats command line option --output-dups <output_dups> pairtools-dedup command line option --output-highcov <output_highcov> pairtools-filterbycov command line option --output-pairs <output_pairs> pairtools-split command line option --output-parsed-alignments <output_parsed_alignments> pairtools-parse command line option pairtools-parse2 command line option --output-profile <output_profile> pairtools command line option --output-rest <output_rest> pairtools-select command line option --output-sam <output_sam> pairtools-split command line option --output-stats <output_stats> pairtools-dedup command line option pairtools-filterbycov command line option pairtools-parse command line option pairtools-parse2 command line option --output-unmapped <output_unmapped> pairtools-dedup command line option pairtools-filterbycov command line option --p1 <p1> pairtools-dedup command line option pairtools-filterbycov command line option --p2 <p2> pairtools-dedup command line option pairtools-filterbycov command line option --pairs, --pairsam pairtools-header-generate command line option --phase-suffixes <phase_suffixes> pairtools-phase command line option --post-mortem pairtools command line option --readid-transform <readid_transform> pairtools-parse command line option pairtools-parse2 command line option --report-alignment-end <report_alignment_end> pairtools-parse command line option --report-orientation <report_orientation> pairtools-parse2 command line option --report-position <report_position> pairtools-parse2 command line option --report-scores, --no-report-scores pairtools-phase command line option --s1 <s1> pairtools-dedup command line option pairtools-filterbycov command line option --s2 <s2> pairtools-dedup command line option pairtools-filterbycov command line option --sam-path <sam_path> pairtools-header-generate command line option --send-header-to <send_header_to> pairtools-dedup command line option pairtools-filterbycov command line option --sep <sep> pairtools-dedup command line option pairtools-filterbycov command line option --single-end pairtools-parse2 command line option --startup-code <startup_code> pairtools-dedup command line option pairtools-select command line option pairtools-stats command line option --tag-mode <tag_mode> pairtools-phase command line option --tmpdir <tmpdir> pairtools-merge command line option pairtools-sort command line option --unmapped-chrom <unmapped_chrom> pairtools-dedup command line option pairtools-filterbycov command line option --version pairtools command line option --view, --regions <view> pairtools-scaling command line option --walks-policy <walks_policy> pairtools-parse command line option --with-chromsizes, --no-chromsizes pairtools-stats command line option --yaml, --no-yaml pairtools-dedup command line option pairtools-stats command line option -c, --chroms-path <chroms_path> pairtools-flip command line option pairtools-parse command line option pairtools-parse2 command line option -c, --columns <columns> pairtools-header-set-columns command line option -c, --reference-columns <reference_columns> pairtools-header-validate-columns command line option -d, --debug pairtools command line option -f, --frags <frags> pairtools-restrict command line option -o, --output <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 -p, --n-proc <n_proc> pairtools-dedup command line option -r, --reference-file <reference_file> pairtools-header-transfer command line option pairtools-header-validate-columns command line option -r, --remove-columns <remove_columns> pairtools-select command line option -s, --seed <seed> pairtools-sample command line option -t, --type-cast <type_cast> pairtools-dedup command line option pairtools-select command line option pairtools-stats command line option -v, --verbose 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 --output-profile <output_profile> --post-mortem --version -d, --debug -v, --verbose pairtools-dedup command line option --backend <backend> --c1 <c1> --c2 <c2> --carryover <carryover> --chrom-subset <chrom_subset> --chunksize <chunksize> --cmd-in <cmd_in> --cmd-out <cmd_out> --engine <engine> --extra-col-pair <extra_col_pair> --filter <filter> --keep-parent-id --mark-dups --max-mismatch <max_mismatch> --method <method> --nproc-in <nproc_in> --nproc-out <nproc_out> --output-bytile-stats <output_bytile_stats> --output-dups <output_dups> --output-stats <output_stats> --output-unmapped <output_unmapped> --p1 <p1> --p2 <p2> --s1 <s1> --s2 <s2> --send-header-to <send_header_to> --sep <sep> --startup-code <startup_code> --unmapped-chrom <unmapped_chrom> --yaml, --no-yaml -o, --output <output> -p, --n-proc <n_proc> -t, --type-cast <type_cast> PAIRS_PATH pairtools-filterbycov command line option --c1 <c1> --c2 <c2> --cmd-in <cmd_in> --cmd-out <cmd_out> --comment-char <comment_char> --mark-multi --max-cov <max_cov> --max-dist <max_dist> --method <method> --nproc-in <nproc_in> --nproc-out <nproc_out> --output-highcov <output_highcov> --output-stats <output_stats> --output-unmapped <output_unmapped> --p1 <p1> --p2 <p2> --s1 <s1> --s2 <s2> --send-header-to <send_header_to> --sep <sep> --unmapped-chrom <unmapped_chrom> -o, --output <output> PAIRS_PATH pairtools-flip command line option --cmd-in <cmd_in> --cmd-out <cmd_out> --nproc-in <nproc_in> --nproc-out <nproc_out> -c, --chroms-path <chroms_path> -o, --output <output> PAIRS_PATH pairtools-header-generate command line option --assembly <assembly> --chroms-path <chroms_path> --cmd-in <cmd_in> --cmd-out <cmd_out> --columns <columns> --extra-columns <extra_columns> --no-flip --nproc-in <nproc_in> --nproc-out <nproc_out> --pairs, --pairsam --sam-path <sam_path> -o, --output <output> PAIRS_PATH pairtools-header-set-columns command line option --cmd-in <cmd_in> --cmd-out <cmd_out> --nproc-in <nproc_in> --nproc-out <nproc_out> -c, --columns <columns> -o, --output <output> PAIRS_PATH pairtools-header-transfer command line option --cmd-in <cmd_in> --cmd-out <cmd_out> --nproc-in <nproc_in> --nproc-out <nproc_out> -o, --output <output> -r, --reference-file <reference_file> PAIRS_PATH pairtools-header-validate-columns command line option --cmd-in <cmd_in> --cmd-out <cmd_out> --nproc-in <nproc_in> --nproc-out <nproc_out> -c, --reference-columns <reference_columns> -o, --output <output> -r, --reference-file <reference_file> PAIRS_PATH pairtools-markasdup command line option --cmd-in <cmd_in> --cmd-out <cmd_out> --nproc-in <nproc_in> --nproc-out <nproc_out> -o, --output <output> PAIRSAM_PATH pairtools-merge command line option --cmd-in <cmd_in> --cmd-out <cmd_out> --compress-program <compress_program> --concatenate, --no-concatenate --keep-first-header, --no-keep-first-header --max-nmerge <max_nmerge> --memory <memory> --nproc <nproc> --nproc-in <nproc_in> --nproc-out <nproc_out> --tmpdir <tmpdir> -o, --output <output> PAIRS_PATH

pairtools-parse command line option --add-columns <add_columns> --add-pair-index --assembly <assembly> --cmd-in <cmd_in> --cmd-out <cmd_out> --drop-readid --drop-sam --drop-seq --flip, --no-flip --max-inter-align-gap <max_inter_align_gap> --max-molecule-size <max_molecule_size> --min-mapq <min_mapq> --nproc-in <nproc_in> --nproc-out <nproc_out> --output-parsed-alignments <output_parsed_alignments> --output-stats <output_stats> --readid-transform <readid_transform> --report-alignment-end <report_alignment_end> --walks-policy <walks_policy> -c, --chroms-path <chroms_path> -o, --output <output> SAM_PATH pairtools-parse2 command line option --add-columns <add_columns> --add-pair-index --assembly <assembly> --cmd-in <cmd_in> --cmd-out <cmd_out> --dedup-max-mismatch <dedup_max_mismatch> --drop-readid, --keep-readid --drop-sam, --keep-sam --drop-seq, --keep-seq --expand, --no-expand --flip, --no-flip --max-expansion-depth <max_expansion_depth> --max-insert-size <max_insert_size> --max-inter-align-gap <max_inter_align_gap> --min-mapq <min_mapq> --nproc-in <nproc_in> --nproc-out <nproc_out> --output-parsed-alignments <output_parsed_alignments> --output-stats <output_stats> --readid-transform <readid_transform> --report-orientation <report_orientation> --report-position <report_position> --single-end -c, --chroms-path <chroms_path> -o, --output <output> SAM_PATH pairtools-phase command line option --clean-output --cmd-in <cmd_in> --cmd-out <cmd_out> --nproc-in <nproc_in> --nproc-out <nproc_out> --phase-suffixes <phase_suffixes> --report-scores, --no-report-scores --tag-mode <tag_mode> -o, --output <output> PAIRS_PATH pairtools-restrict command line option --cmd-in <cmd_in> --cmd-out <cmd_out> --nproc-in <nproc_in> --nproc-out <nproc_out> -f, --frags <frags> -o, --output <output> PAIRS_PATH pairtools-sample command line option --cmd-in <cmd_in> --cmd-out <cmd_out> --nproc-in <nproc_in> --nproc-out <nproc_out> -o, --output <output> -s, --seed <seed> FRACTION PAIRS_PATH pairtools-scaling command line option --chunksize <chunksize> --cmd-in <cmd_in> --cmd-out <cmd_out> --dist-range <dist_range> --n-dist-bins <n_dist_bins> --nproc-in <nproc_in> --nproc-out <nproc_out> --view, --regions <view> -o, --output <output> INPUT_PATH pairtools-select command line option --chrom-subset <chrom_subset> --cmd-in <cmd_in> --cmd-out <cmd_out> --nproc-in <nproc_in> --nproc-out <nproc_out> --output-rest <output_rest> --startup-code <startup_code> -o, --output <output> -r, --remove-columns <remove_columns> -t, --type-cast <type_cast> CONDITION PAIRS_PATH pairtools-sort command line option --cmd-in <cmd_in> --cmd-out <cmd_out> --compress-program <compress_program> --memory <memory> --nproc <nproc> --nproc-in <nproc_in> --nproc-out <nproc_out> --tmpdir <tmpdir> -o, --output <output> PAIRS_PATH pairtools-split command line option --cmd-in <cmd_in> --cmd-out <cmd_out> --nproc-in <nproc_in> --nproc-out <nproc_out> --output-pairs <output_pairs> --output-sam <output_sam> PAIRSAM_PATH pairtools-stats command line option --bytile-dups, --no-bytile-dups --chrom-subset <chrom_subset> --cmd-in <cmd_in> --cmd-out <cmd_out> --engine <engine> --filter <filter> --merge --nproc-in <nproc_in> --nproc-out <nproc_out> --output-bytile-stats <output_bytile_stats> --startup-code <startup_code> --with-chromsizes, --no-chromsizes --yaml, --no-yaml -o, --output <output> -t, --type-cast <type_cast> INPUT_PATH

S

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