| Previous changeset 3:5412142130ad (2024-04-16) Next changeset 5:56bb29747b4d (2024-05-21) |
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Commit message:
planemo upload for repository https://github.com/open2c/pairtools commit 162c595b19e442f40be4c2f5434b20b56ade52d4 |
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modified:
dedup.xml macros.xml test-data/output_dedup_pairs.pairsam test-data/output_dedup_pairs.stats test-data/output_dedup_pairs_markdups.pairsam test-data/output_dedup_sorted.pairsam test-data/output_dups_pairs_markdups.pairsam test-data/output_pairs_split.bam test-data/output_pairs_split.pairs test-data/output_parsed_pairs.stats test-data/output_parsed_pairs_bam.pairs test-data/output_parsed_pairs_bam_5unique.pairs test-data/output_parsed_pairs_bam_min_mapq_40.pairs test-data/output_parsed_pairs_bam_readid_dropped.pairs test-data/output_parsed_pairs_bam_readid_dropped_seq.pairs test-data/output_parsed_pairs_sam.pairs test-data/output_parsed_pairs_sam_assemblyname.pairs test-data/output_sorted_pairs.pairs test-data/pairs_output.stats test-data/pairs_output_merged.stats test-data/pairs_output_with_chromsize.stats test-data/pairs_output_yaml.stats |
| b |
| diff -r 5412142130ad -r 55a53b5e308d dedup.xml --- a/dedup.xml Tue Apr 16 12:51:21 2024 +0000 +++ b/dedup.xml Tue Apr 30 12:02:29 2024 +0000 |
| b |
| @@ -20,7 +20,7 @@ ]]></command> <inputs> <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/> - <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="False" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/> + <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="True" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/> <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/> <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/> </inputs> |
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| diff -r 5412142130ad -r 55a53b5e308d macros.xml --- a/macros.xml Tue Apr 16 12:51:21 2024 +0000 +++ b/macros.xml Tue Apr 30 12:02:29 2024 +0000 |
| b |
| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.0.3</token> + <token name="@TOOL_VERSION@">1.1.0</token> <token name="@SUFFIX_VERSION@">0</token> <xml name="edam_ontology"> <edam_datas> |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_dedup_pairs.pairsam --- a/test-data/output_dedup_pairs.pairsam Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_dedup_pairs.pairsam Tue Apr 30 12:02:29 2024 +0000 |
| b |
| @@ -39,20 +39,20 @@ #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FHNM:i:0MD:Z:35AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15566:24141145chrI33506050M=3199-201TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCGHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:18861:21891 chrI 35431 chrI 35703 + - UU HWI-ST560:29:B0A7LABXX:2:1101:18861:2189197chrI354316050M=35654273GACCACGTGGTCGTTGATGCTGCCAGCAGTTGTGCAGACCTGCATTGCTG114442222322<2@FEAFHFH<CFHFFH?GH:CDHGGIGEFDG<BBH9?NM:i:1MD:Z:35G14AS:i:45XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:18861:21891145chrI356546050M=35431-273ATGTGGCTGCTTTAATTGAGCCTCTTTCTGTCACCTGGCATGCTGTTAAG>EGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFD<HFFDDDDB@BNM:i:1MD:Z:14G35AS:i:45XS:i:0Yt:Z:UU |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_dedup_pairs.stats --- a/test-data/output_dedup_pairs.stats Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_dedup_pairs.stats Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -28,6 +28,33 @@\n summary/frac_cis_40kb+\t0.058823529411764705\n summary/frac_dups\t0.011378002528445006\n summary/complexity_naive\t34495.88583157276\n+summary/dist_freq_convergence/convergence_dist\t1333521\n+summary/dist_freq_convergence/strands_w_max_convergence_dist\t++\n+summary/dist_freq_convergence/convergence_rel_diff_threshold\t0.05\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/++\t49\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/--\t58\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/-+\t65\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/+-\t425\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist_all_strands\t597\n+summary/dist_freq_convergence/n_cis_pairs_above_convergence_dist_all_strands\t0\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/++\t0.08207705192629816\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/--\t0.09715242881072027\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/-+\t0.10887772194304858\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/+-\t0.711892797319933\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_cis_in_cis_above_convergence_dist_all_strands\t0.0\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/++\t0.061946902654867256\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/--\t0.07332490518331226\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/-+\t0.08217446270543616\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/+-\t0.5372945638432364\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist_all_strands\t0.754740834386852\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_above_convergence_dist_all_strands\t0.0\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/++\t0.06265984654731457\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/--\t0.0741687979539642\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/-+\t0.08312020460358056\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/+-\t0.5434782608695652\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist_all_strands\t0.7634271099744245\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_above_convergence_dist_all_strands\t0.0\n chrom_freq/chrIV/chrIV\t83\n chrom_freq/chrVII/chrVII\t55\n chrom_freq/chrXV/chrXV\t53\n@@ -133,143 +160,279 @@\n dist_freq/2-3/-+\t0\n dist_freq/2-3/--\t0\n dist_freq/2-3/++\t0\n-dist_freq/3-6/+-\t0\n-dist_freq/3-6/-+\t1\n-dist_freq/3-6/--\t0\n-dist_freq/3-6/++\t1\n-dist_freq/6-10/+-\t0\n-dist_freq/6-10/-+\t0\n-dist_freq/6-10/--\t0\n-dist_freq/6-10/++\t0\n-dist_freq/10-18/+-\t0\n-dist_freq/10-18/-+\t0\n-dist_freq/10-18/--\t0\n-dist_freq/10-18/++\t0\n-dist_freq/18-32/+-\t0\n-dist_freq/18-32/-+\t0\n-dist_freq/18-32/--\t0\n-dist_freq/18-32/++\t0\n-dist_freq/32-56/+-\t0\n-dist_freq/32-56/-+\t0\n-dist_freq/32-56/--\t0\n-dist_freq/32-56/++\t0\n-dist_freq/56-100/+-\t0\n-dist_freq/56-100/-+\t1\n-dist_freq/56-100/--\t0\n-dist_freq/56-100/++\t0\n-dist_freq/100-178/+-\t7\n-dist_freq/100-178/-+\t2\n-dist_freq/100-178/--\t2\n-dist_freq/100-178/++\t0\n-dist_freq/178-316/+-\t334\n-dist_freq/178-316/-+\t9\n-dist_freq/178-316/--\t1\n-dist_freq/178-316/++\t0\n-dist_freq/316-562/+-\t34\n-dist_freq/316-562/-+\t7\n-dist_freq/316-562/--\t0\n-dist_freq/316-562/++\t0\n-dist_freq/562-1000/+-\t1\n-dist_freq/562-1000/-+\t11\n-dist_freq/562-1000/--\t0\n-dist_freq/562-1000/++\t1\n-dist_freq/1000-1778/+-\t0\n-dist_freq/1000-1778/-+\t5\n-dist_freq/1000-1778/--\t6\n-dist_freq/1000-1778/++\t1\n-dist_freq/1778-3162/+-\t5\n-dist_freq/1778-3162/-+\t7\n-dist_freq/1778-3162/--\t2\n-dist_freq/1778-3162/++\t0\n-dist_freq/3162-5623/+-\t4\n-dist_freq/3162-5623/-+\t4\n-dist_freq/3162-5623/--\t6\n-dist_freq/3162-5623/++\t4\n-dist_freq/5623-10000/+-\t9\n-dist_freq/5623-10000/-+\t4\n-d'..b'7/++\t2\n+dist_freq/237137-316228/+-\t1\n+dist_freq/237137-316228/-+\t0\n+dist_freq/237137-316228/--\t0\n+dist_freq/237137-316228/++\t1\n+dist_freq/316228-421697/+-\t0\n+dist_freq/316228-421697/-+\t0\n+dist_freq/316228-421697/--\t0\n+dist_freq/316228-421697/++\t0\n+dist_freq/421697-562341/+-\t0\n+dist_freq/421697-562341/-+\t0\n+dist_freq/421697-562341/--\t0\n+dist_freq/421697-562341/++\t1\n+dist_freq/562341-749894/+-\t1\n+dist_freq/562341-749894/-+\t0\n+dist_freq/562341-749894/--\t0\n+dist_freq/562341-749894/++\t1\n+dist_freq/749894-1000000/+-\t0\n+dist_freq/749894-1000000/-+\t0\n+dist_freq/749894-1000000/--\t0\n+dist_freq/749894-1000000/++\t0\n+dist_freq/1000000-1333521/+-\t0\n+dist_freq/1000000-1333521/-+\t0\n+dist_freq/1000000-1333521/--\t1\n+dist_freq/1000000-1333521/++\t0\n+dist_freq/1333521-1778279/+-\t0\n+dist_freq/1333521-1778279/-+\t0\n+dist_freq/1333521-1778279/--\t0\n+dist_freq/1333521-1778279/++\t0\n+dist_freq/1778279-2371374/+-\t0\n+dist_freq/1778279-2371374/-+\t0\n+dist_freq/1778279-2371374/--\t0\n+dist_freq/1778279-2371374/++\t0\n+dist_freq/2371374-3162278/+-\t0\n+dist_freq/2371374-3162278/-+\t0\n+dist_freq/2371374-3162278/--\t0\n+dist_freq/2371374-3162278/++\t0\n+dist_freq/3162278-4216965/+-\t0\n+dist_freq/3162278-4216965/-+\t0\n+dist_freq/3162278-4216965/--\t0\n+dist_freq/3162278-4216965/++\t0\n+dist_freq/4216965-5623413/+-\t0\n+dist_freq/4216965-5623413/-+\t0\n+dist_freq/4216965-5623413/--\t0\n+dist_freq/4216965-5623413/++\t0\n+dist_freq/5623413-7498942/+-\t0\n+dist_freq/5623413-7498942/-+\t0\n+dist_freq/5623413-7498942/--\t0\n+dist_freq/5623413-7498942/++\t0\n+dist_freq/7498942-10000000/+-\t0\n+dist_freq/7498942-10000000/-+\t0\n+dist_freq/7498942-10000000/--\t0\n+dist_freq/7498942-10000000/++\t0\n+dist_freq/10000000-13335214/+-\t0\n+dist_freq/10000000-13335214/-+\t0\n+dist_freq/10000000-13335214/--\t0\n+dist_freq/10000000-13335214/++\t0\n+dist_freq/13335214-17782794/+-\t0\n+dist_freq/13335214-17782794/-+\t0\n+dist_freq/13335214-17782794/--\t0\n+dist_freq/13335214-17782794/++\t0\n+dist_freq/17782794-23713737/+-\t0\n+dist_freq/17782794-23713737/-+\t0\n+dist_freq/17782794-23713737/--\t0\n+dist_freq/17782794-23713737/++\t0\n+dist_freq/23713737-31622777/+-\t0\n+dist_freq/23713737-31622777/-+\t0\n+dist_freq/23713737-31622777/--\t0\n+dist_freq/23713737-31622777/++\t0\n+dist_freq/31622777-42169650/+-\t0\n+dist_freq/31622777-42169650/-+\t0\n+dist_freq/31622777-42169650/--\t0\n+dist_freq/31622777-42169650/++\t0\n+dist_freq/42169650-56234133/+-\t0\n+dist_freq/42169650-56234133/-+\t0\n+dist_freq/42169650-56234133/--\t0\n+dist_freq/42169650-56234133/++\t0\n+dist_freq/56234133-74989421/+-\t0\n+dist_freq/56234133-74989421/-+\t0\n+dist_freq/56234133-74989421/--\t0\n+dist_freq/56234133-74989421/++\t0\n+dist_freq/74989421-100000000/+-\t0\n+dist_freq/74989421-100000000/-+\t0\n+dist_freq/74989421-100000000/--\t0\n+dist_freq/74989421-100000000/++\t0\n+dist_freq/100000000-133352143/+-\t0\n+dist_freq/100000000-133352143/-+\t0\n+dist_freq/100000000-133352143/--\t0\n+dist_freq/100000000-133352143/++\t0\n+dist_freq/133352143-177827941/+-\t0\n+dist_freq/133352143-177827941/-+\t0\n+dist_freq/133352143-177827941/--\t0\n+dist_freq/133352143-177827941/++\t0\n+dist_freq/177827941-237137371/+-\t0\n+dist_freq/177827941-237137371/-+\t0\n+dist_freq/177827941-237137371/--\t0\n+dist_freq/177827941-237137371/++\t0\n+dist_freq/237137371-316227766/+-\t0\n+dist_freq/237137371-316227766/-+\t0\n+dist_freq/237137371-316227766/--\t0\n+dist_freq/237137371-316227766/++\t0\n+dist_freq/316227766-421696503/+-\t0\n+dist_freq/316227766-421696503/-+\t0\n+dist_freq/316227766-421696503/--\t0\n+dist_freq/316227766-421696503/++\t0\n+dist_freq/421696503-562341325/+-\t0\n+dist_freq/421696503-562341325/-+\t0\n+dist_freq/421696503-562341325/--\t0\n+dist_freq/421696503-562341325/++\t0\n+dist_freq/562341325-749894209/+-\t0\n+dist_freq/562341325-749894209/-+\t0\n+dist_freq/562341325-749894209/--\t0\n+dist_freq/562341325-749894209/++\t0\n+dist_freq/749894209-1000000000/+-\t0\n+dist_freq/749894209-1000000000/-+\t0\n+dist_freq/749894209-1000000000/--\t0\n+dist_freq/749894209-1000000000/++\t0\n+dist_freq/1000000000+/+-\t0\n+dist_freq/1000000000+/-+\t0\n+dist_freq/1000000000+/--\t0\n+dist_freq/1000000000+/++\t0\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_dedup_pairs_markdups.pairsam --- a/test-data/output_dedup_pairs_markdups.pairsam Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_dedup_pairs_markdups.pairsam Tue Apr 30 12:02:29 2024 +0000 |
| b |
| @@ -39,20 +39,20 @@ #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FHNM:i:0MD:Z:35AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15566:24141145chrI33506050M=3199-201TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCGHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:18861:21891 chrI 35431 chrI 35703 + - UU HWI-ST560:29:B0A7LABXX:2:1101:18861:2189197chrI354316050M=35654273GACCACGTGGTCGTTGATGCTGCCAGCAGTTGTGCAGACCTGCATTGCTG114442222322<2@FEAFHFH<CFHFFH?GH:CDHGGIGEFDG<BBH9?NM:i:1MD:Z:35G14AS:i:45XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:18861:21891145chrI356546050M=35431-273ATGTGGCTGCTTTAATTGAGCCTCTTTCTGTCACCTGGCATGCTGTTAAG>EGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFD<HFFDDDDB@BNM:i:1MD:Z:14G35AS:i:45XS:i:0Yt:Z:UU |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_dedup_sorted.pairsam --- a/test-data/output_dedup_sorted.pairsam Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_dedup_sorted.pairsam Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -39,24 +39,24 @@\n #samheader: @PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz\n #samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam\tPP:bwa\tVN:1.0.2\n #samheader: @PG\tID:pairtools_sort-1.3\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-1.2\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_dedup-1.4\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-1.3\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_sort-1.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/c/1/c/dataset_c1c8eade-049e-4209-b8f9-a97c31df8468.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/4/outputs/dataset_22fb7731-5e54-4b91-9180-5373e3456c9c.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-1.4\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_dedup-1.4\tPN:pairtools_dedup\tCL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-1.3\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-1.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-1.4\tVN:1.1.0\n #samheader: @PG\tID:bwa-2CCE5976\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz\n #samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam\tPP:bwa-2CCE5976\tVN:1.0.2\n #samheader: @PG\tID:pairtools_sort-2.3\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-2.2\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_dedup-2.4\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-2.3\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_sort-2.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/c/1/c/dataset_c1c8eade-049e-4209-b8f9-a97c31df8468.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/4/outputs/dataset_22fb7731-5e54-4b91-9180-5373e3456c9c.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-2.4\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_dedup-2.4\tPN:pairtools_dedup\tCL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-2.3\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-2.5\tPN:pairtools_sort\tCL:/usr/lo'..b'0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-3.3\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-3.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-3.4\tVN:1.1.0\n #samheader: @PG\tID:bwa-4548A671\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz\n #samheader: @PG\tID:samtools\tPN:samtools\tPP:bwa-4548A671\tVN:1.19.2\tCL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam\n #samheader: @PG\tID:pairtools_parse-4.3\tPN:pairtools_parse\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam\tPP:samtools\tVN:1.0.2\n #samheader: @PG\tID:pairtools_sort-4.4\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-4.3\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_dedup-4.5\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-4.4\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_sort-4.6\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/c/1/c/dataset_c1c8eade-049e-4209-b8f9-a97c31df8468.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/4/outputs/dataset_22fb7731-5e54-4b91-9180-5373e3456c9c.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-4.5\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_dedup-4.5\tPN:pairtools_dedup\tCL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-4.4\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-4.6\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-4.5\tVN:1.1.0\n #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2\n HWI-ST560:29:B0A7LABXX:2:1101:15566:24141\tchrI\t3199\tchrI\t3399\t+\t-\tUU\tHWI-ST560:29:B0A7LABXX:2:1101:15566:24141\x1997\x19chrI\x193199\x1960\x1915S35M\x19=\x193350\x19201\x19CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA\x19111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FH\x19NM:i:0\x19MD:Z:35\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:15566:24141\x19145\x19chrI\x193350\x1960\x1950M\x19=\x193199\x19-201\x19TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATC\x19GHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==\x19NM:i:0\x19MD:Z:50\x19AS:i:50\x19XS:i:0\x19Yt:Z:UU\n HWI-ST560:29:B0A7LABXX:2:1101:18861:21891\tchrI\t35431\tchrI\t35703\t+\t-\tUU\tHWI-ST560:29:B0A7LABXX:2:1101:18861:21891\x1997\x19chrI\x1935431\x1960\x1950M\x19=\x1935654\x19273\x19GACCACGTGGTCGTTGATGCTGCCAGCAGTTGTGCAGACCTGCATTGCTG\x19114442222322<2@FEAFHFH<CFHFFH?GH:CDHGGIGEFDG<BBH9?\x19NM:i:1\x19MD:Z:35G14\x19AS:i:45\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:18861:21891\x19145\x19chrI\x1935654\x1960\x1950M\x19=\x1935431\x19-273\x19ATGTGGCTGCTTTAATTGAGCCTCTTTCTGTCACCTGGCATGCTGTTAAG\x19>EGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFD<HFFDDDDB@B\x19NM:i:1\x19MD:Z:14G35\x19AS:i:45\x19XS:i:0\x19Yt:Z:UU\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_dups_pairs_markdups.pairsam --- a/test-data/output_dups_pairs_markdups.pairsam Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_dups_pairs_markdups.pairsam Tue Apr 30 12:02:29 2024 +0000 |
| b |
| @@ -39,20 +39,20 @@ #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --output-dups output_dups_pairs_markdups.pairsam --mark-dups output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --output-dups output_dups_pairs_markdups.pairsam --mark-dups output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --output-dups output_dups_pairs_markdups.pairsam --mark-dups output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --output-dups output_dups_pairs_markdups.pairsam --mark-dups output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWI-ST560:29:B0A7LABXX:2:1101:2692:4382 chrIII 80421 chrIII 80656 + - DD HWI-ST560:29:B0A7LABXX:2:1101:2692:4382161chrIII804216050M=80607236CTCTTCTAGCAGGAAGAGATCGTCCTTTTTACTGTCCTCGAATCCTACCGCCCFFFFFHHHHHGIIGIGIJIIJJJJJJJJIJJIJJIJJJIJIIFIJIINM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:2692:438281chrIII806076050M=80421-236ATCTTATATGCCTAATACAAAAAGAAGCTCACTAACATCAAAATCATTATHIGGFIIGIIJJJJJIHJJJJHHFIJJIHIFIJJJHGCC>332224D=:1NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:2403:20808 chrIV 497939 chrIV 498215 + - DD HWUSI-EAS1533_0033_FC:1:1:2403:2080897chrIV4979396036M=498180277CGCTTTCATTACTCGAATCCGTCAAAGACGCTTCTT4544588888C@@CC@CCC@@@C@@@C@CCC@C@CCNM:i:1MD:Z:0A35AS:i:35XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:2403:20808145chrIV4981806036M=497939-277GGCTGGTGAAGGAGTATTATTTACAATTCTAAAGCN@@C@@@@CC@CC@CC22C@@@CCCCC888886666)NM:i:1MD:Z:35T0AS:i:35XS:i:0Yt:Z:UU |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_pairs_split.bam |
| b |
| Binary file test-data/output_pairs_split.bam has changed |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_pairs_split.pairs --- a/test-data/output_pairs_split.pairs Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_pairs_split.pairs Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -39,24 +39,24 @@\n #samheader: @PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz\n #samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam\tPP:bwa\tVN:1.0.2\n #samheader: @PG\tID:pairtools_sort-1.3\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-1.2\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_dedup-1.4\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-1.3\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_split-1.5\tPN:pairtools_split\tCL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-1.4\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_dedup-1.4\tPN:pairtools_dedup\tCL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-1.3\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_split-1.5\tPN:pairtools_split\tCL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-1.4\tVN:1.1.0\n #samheader: @PG\tID:bwa-2CCE5976\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz\n #samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam\tPP:bwa-2CCE5976\tVN:1.0.2\n #samheader: @PG\tID:pairtools_sort-2.3\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-2.2\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_dedup-2.4\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-2.3\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_split-2.5\tPN:pairtools_split\tCL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-2.4\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_dedup-2.4\tPN:pairtools_dedup\tCL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --'..b'up-3.4\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-3.3\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_split-3.5\tPN:pairtools_split\tCL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-3.4\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_dedup-3.4\tPN:pairtools_dedup\tCL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-3.3\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_split-3.5\tPN:pairtools_split\tCL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-3.4\tVN:1.1.0\n #samheader: @PG\tID:bwa-4548A671\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz\n #samheader: @PG\tID:samtools\tPN:samtools\tPP:bwa-4548A671\tVN:1.19.2\tCL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam\n #samheader: @PG\tID:pairtools_parse-4.3\tPN:pairtools_parse\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam\tPP:samtools\tVN:1.0.2\n #samheader: @PG\tID:pairtools_sort-4.4\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-4.3\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_dedup-4.5\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-4.4\tVN:1.0.2\n-#samheader: @PG\tID:pairtools_split-4.6\tPN:pairtools_split\tCL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-4.5\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_dedup-4.5\tPN:pairtools_dedup\tCL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-4.4\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_split-4.6\tPN:pairtools_split\tCL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-4.5\tVN:1.1.0\n #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type\n HWI-ST560:29:B0A7LABXX:2:1101:15566:24141\tchrI\t3199\tchrI\t3399\t+\t-\tUU\n HWI-ST560:29:B0A7LABXX:2:1101:18861:21891\tchrI\t35431\tchrI\t35703\t+\t-\tUU\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_parsed_pairs.stats --- a/test-data/output_parsed_pairs.stats Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_parsed_pairs.stats Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -6,16 +6,14 @@\n total_nodups\t308\n cis\t308\n trans\t0\n-pair_types/MU\t88\n+pair_types/MU\t95\n pair_types/UU\t293\n pair_types/MM\t49\n pair_types/UR\t8\n pair_types/MR\t26\n pair_types/NR\t110\n pair_types/RU\t7\n-pair_types/nM\t3\n-pair_types/Mu\t7\n-pair_types/NM\t1\n+pair_types/NM\t4\n cis_1kb+\t15\n cis_2kb+\t14\n cis_4kb+\t14\n@@ -31,6 +29,33 @@\n summary/frac_cis_40kb+\t0.02922077922077922\n summary/frac_dups\t0.0\n summary/complexity_naive\tnan\n+summary/dist_freq_convergence/convergence_dist\t177828\n+summary/dist_freq_convergence/strands_w_max_convergence_dist\t++\n+summary/dist_freq_convergence/convergence_rel_diff_threshold\t0.05\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/++\t4\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/--\t2\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/-+\t1\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/+-\t301\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist_all_strands\t308\n+summary/dist_freq_convergence/n_cis_pairs_above_convergence_dist_all_strands\t0\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/++\t0.012987012987012988\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/--\t0.006493506493506494\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/-+\t0.003246753246753247\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/+-\t0.9772727272727273\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_cis_in_cis_above_convergence_dist_all_strands\t0.0\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/++\t0.012987012987012988\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/--\t0.006493506493506494\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/-+\t0.003246753246753247\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/+-\t0.9772727272727273\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_above_convergence_dist_all_strands\t0.0\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/++\t0.012987012987012988\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/--\t0.006493506493506494\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/-+\t0.003246753246753247\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/+-\t0.9772727272727273\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_above_convergence_dist_all_strands\t0.0\n chrom_freq/Test_seq/Test_seq\t308\n dist_freq/0-1/+-\t0\n dist_freq/0-1/-+\t0\n@@ -44,143 +69,279 @@\n dist_freq/2-3/-+\t0\n dist_freq/2-3/--\t0\n dist_freq/2-3/++\t0\n-dist_freq/3-6/+-\t0\n-dist_freq/3-6/-+\t0\n-dist_freq/3-6/--\t0\n-dist_freq/3-6/++\t0\n-dist_freq/6-10/+-\t0\n-dist_freq/6-10/-+\t0\n-dist_freq/6-10/--\t0\n-dist_freq/6-10/++\t0\n-dist_freq/10-18/+-\t0\n-dist_freq/10-18/-+\t0\n-dist_freq/10-18/--\t0\n-dist_freq/10-18/++\t0\n-dist_freq/18-32/+-\t0\n-dist_freq/18-32/-+\t0\n-dist_freq/18-32/--\t0\n-dist_freq/18-32/++\t0\n-dist_freq/32-56/+-\t0\n-dist_freq/32-56/-+\t0\n-dist_freq/32-56/--\t0\n-dist_freq/32-56/++\t0\n-dist_freq/56-100/+-\t1\n-dist_freq/56-100/-+\t0\n-dist_freq/56-100/--\t0\n-dist_freq/56-100/++\t0\n-dist_freq/100-178/+-\t3\n-dist_freq/100-178/-+\t0\n-dist_freq/100-178/--\t0\n-dist_freq/100-178/++\t0\n-dist_freq/178-316/+-\t53\n-dist_freq/178-316/-+\t0\n-dist_freq/178-316/--\t0\n-dist_freq/178-316/++\t0\n-dist_freq/316-562/+-\t236\n-dist_freq/316-562/-+\t0\n-dist_freq/316-562/--\t0\n-dist_freq/316-562/++\t0\n-dist_freq/562-1000/+-\t0\n-dist_freq/562-1000/-+\t0\n-dist_freq/562-1000/--\t0\n-dist_freq/562-1000/++\t0\n-dist_freq/1000-1778/+-\t1\n-dist_freq/1000-1778/-+\t0\n-dist_freq/1000-1778/--\t0\n-dist_freq/1000-1778/++\t0\n-dist_freq/1778-3162/+-\t0\n'..b'7/++\t0\n+dist_freq/237137-316228/+-\t0\n+dist_freq/237137-316228/-+\t0\n+dist_freq/237137-316228/--\t0\n+dist_freq/237137-316228/++\t0\n+dist_freq/316228-421697/+-\t0\n+dist_freq/316228-421697/-+\t0\n+dist_freq/316228-421697/--\t0\n+dist_freq/316228-421697/++\t0\n+dist_freq/421697-562341/+-\t0\n+dist_freq/421697-562341/-+\t0\n+dist_freq/421697-562341/--\t0\n+dist_freq/421697-562341/++\t0\n+dist_freq/562341-749894/+-\t0\n+dist_freq/562341-749894/-+\t0\n+dist_freq/562341-749894/--\t0\n+dist_freq/562341-749894/++\t0\n+dist_freq/749894-1000000/+-\t0\n+dist_freq/749894-1000000/-+\t0\n+dist_freq/749894-1000000/--\t0\n+dist_freq/749894-1000000/++\t0\n+dist_freq/1000000-1333521/+-\t0\n+dist_freq/1000000-1333521/-+\t0\n+dist_freq/1000000-1333521/--\t0\n+dist_freq/1000000-1333521/++\t0\n+dist_freq/1333521-1778279/+-\t0\n+dist_freq/1333521-1778279/-+\t0\n+dist_freq/1333521-1778279/--\t0\n+dist_freq/1333521-1778279/++\t0\n+dist_freq/1778279-2371374/+-\t0\n+dist_freq/1778279-2371374/-+\t0\n+dist_freq/1778279-2371374/--\t0\n+dist_freq/1778279-2371374/++\t0\n+dist_freq/2371374-3162278/+-\t0\n+dist_freq/2371374-3162278/-+\t0\n+dist_freq/2371374-3162278/--\t0\n+dist_freq/2371374-3162278/++\t0\n+dist_freq/3162278-4216965/+-\t0\n+dist_freq/3162278-4216965/-+\t0\n+dist_freq/3162278-4216965/--\t0\n+dist_freq/3162278-4216965/++\t0\n+dist_freq/4216965-5623413/+-\t0\n+dist_freq/4216965-5623413/-+\t0\n+dist_freq/4216965-5623413/--\t0\n+dist_freq/4216965-5623413/++\t0\n+dist_freq/5623413-7498942/+-\t0\n+dist_freq/5623413-7498942/-+\t0\n+dist_freq/5623413-7498942/--\t0\n+dist_freq/5623413-7498942/++\t0\n+dist_freq/7498942-10000000/+-\t0\n+dist_freq/7498942-10000000/-+\t0\n+dist_freq/7498942-10000000/--\t0\n+dist_freq/7498942-10000000/++\t0\n+dist_freq/10000000-13335214/+-\t0\n+dist_freq/10000000-13335214/-+\t0\n+dist_freq/10000000-13335214/--\t0\n+dist_freq/10000000-13335214/++\t0\n+dist_freq/13335214-17782794/+-\t0\n+dist_freq/13335214-17782794/-+\t0\n+dist_freq/13335214-17782794/--\t0\n+dist_freq/13335214-17782794/++\t0\n+dist_freq/17782794-23713737/+-\t0\n+dist_freq/17782794-23713737/-+\t0\n+dist_freq/17782794-23713737/--\t0\n+dist_freq/17782794-23713737/++\t0\n+dist_freq/23713737-31622777/+-\t0\n+dist_freq/23713737-31622777/-+\t0\n+dist_freq/23713737-31622777/--\t0\n+dist_freq/23713737-31622777/++\t0\n+dist_freq/31622777-42169650/+-\t0\n+dist_freq/31622777-42169650/-+\t0\n+dist_freq/31622777-42169650/--\t0\n+dist_freq/31622777-42169650/++\t0\n+dist_freq/42169650-56234133/+-\t0\n+dist_freq/42169650-56234133/-+\t0\n+dist_freq/42169650-56234133/--\t0\n+dist_freq/42169650-56234133/++\t0\n+dist_freq/56234133-74989421/+-\t0\n+dist_freq/56234133-74989421/-+\t0\n+dist_freq/56234133-74989421/--\t0\n+dist_freq/56234133-74989421/++\t0\n+dist_freq/74989421-100000000/+-\t0\n+dist_freq/74989421-100000000/-+\t0\n+dist_freq/74989421-100000000/--\t0\n+dist_freq/74989421-100000000/++\t0\n+dist_freq/100000000-133352143/+-\t0\n+dist_freq/100000000-133352143/-+\t0\n+dist_freq/100000000-133352143/--\t0\n+dist_freq/100000000-133352143/++\t0\n+dist_freq/133352143-177827941/+-\t0\n+dist_freq/133352143-177827941/-+\t0\n+dist_freq/133352143-177827941/--\t0\n+dist_freq/133352143-177827941/++\t0\n+dist_freq/177827941-237137371/+-\t0\n+dist_freq/177827941-237137371/-+\t0\n+dist_freq/177827941-237137371/--\t0\n+dist_freq/177827941-237137371/++\t0\n+dist_freq/237137371-316227766/+-\t0\n+dist_freq/237137371-316227766/-+\t0\n+dist_freq/237137371-316227766/--\t0\n+dist_freq/237137371-316227766/++\t0\n+dist_freq/316227766-421696503/+-\t0\n+dist_freq/316227766-421696503/-+\t0\n+dist_freq/316227766-421696503/--\t0\n+dist_freq/316227766-421696503/++\t0\n+dist_freq/421696503-562341325/+-\t0\n+dist_freq/421696503-562341325/-+\t0\n+dist_freq/421696503-562341325/--\t0\n+dist_freq/421696503-562341325/++\t0\n+dist_freq/562341325-749894209/+-\t0\n+dist_freq/562341325-749894209/-+\t0\n+dist_freq/562341325-749894209/--\t0\n+dist_freq/562341325-749894209/++\t0\n+dist_freq/749894209-1000000000/+-\t0\n+dist_freq/749894209-1000000000/-+\t0\n+dist_freq/749894209-1000000000/--\t0\n+dist_freq/749894209-1000000000/++\t0\n+dist_freq/1000000000+/+-\t0\n+dist_freq/1000000000+/-+\t0\n+dist_freq/1000000000+/--\t0\n+dist_freq/1000000000+/++\t0\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_parsed_pairs_bam.pairs --- a/test-data/output_parsed_pairs_bam.pairs Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_parsed_pairs_bam.pairs Tue Apr 30 12:02:29 2024 +0000 |
| b |
| @@ -37,14 +37,14 @@ #samheader: @SQ SN:chrXV LN:1091291 #samheader: @SQ SN:chrXVI LN:948066 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.0.3 +#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz -#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam -#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.0.3 +#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWI-ST560:29:B0A7LABXX:2:1101:5084:4188 ! 0 ! 0 - - NM HWI-ST560:29:B0A7LABXX:2:1101:5084:4188133chrI24200*=24200GGAACCGTAAAGGTTTATCGCGGTAGTAGTTTTTCACACGATTCGATAAA?<@DFDFD=FBHHCBHGGIJIIG:C@DGD??DDH?FHGHIJJDGCGEGG;AS:i:0XS:i:0Yt:Z:NM HWI-ST560:29:B0A7LABXX:2:1101:5084:418873chrI242009S41M=24200TTGATAGACTTCGTATGTGGAGTACTGTTTTATGGCGCTTATGTGTATTC11144222222322<<C<IHGHAEFCHEHHIHGCGHHHIIEGGGBB<<9?NM:i:0MD:Z:41AS:i:41XS:i:40XA:Z:chrXIV,-781623,50M,2;chrXI,+2426,50M,3;chrX,+9383,50M,3;chrIX,+9400,50M,3;Yt:Z:NM HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FHNM:i:0MD:Z:35AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15566:24141145chrI33506050M=3199-201TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCGHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_parsed_pairs_bam_5unique.pairs --- a/test-data/output_parsed_pairs_bam_5unique.pairs Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_parsed_pairs_bam_5unique.pairs Tue Apr 30 12:02:29 2024 +0000 |
| b |
| @@ -37,14 +37,14 @@ #samheader: @SQ SN:chrXV LN:1091291 #samheader: @SQ SN:chrXVI LN:948066 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/a/a/0/dataset_aa06559a-c31e-4f53-9ca1-50c7b65e2a6a.dat -c /tmp/tmpvtvmbj0m/files/6/0/7/dataset_6076d2d8-04ad-454f-b0d1-b44203c217ae.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/15/outputs/dataset_8206c374-986e-4a2d-883d-826510572fd0.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.0.3 +#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/7/8/e/dataset_78e4da88-6bc8-43af-bfe6-8d37906fee0f.dat -c /tmp/tmpchj83off/files/5/3/5/dataset_535439dd-341d-4e21-9286-84aa079d5b25.dat -o /tmp/tmpchj83off/job_working_directory/000/15/outputs/dataset_de499407-bd0d-4497-a7ae-58bd962252d3.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz -#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/a/a/0/dataset_aa06559a-c31e-4f53-9ca1-50c7b65e2a6a.dat -c /tmp/tmpvtvmbj0m/files/6/0/7/dataset_6076d2d8-04ad-454f-b0d1-b44203c217ae.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/15/outputs/dataset_8206c374-986e-4a2d-883d-826510572fd0.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/7/8/e/dataset_78e4da88-6bc8-43af-bfe6-8d37906fee0f.dat -c /tmp/tmpchj83off/files/5/3/5/dataset_535439dd-341d-4e21-9286-84aa079d5b25.dat -o /tmp/tmpchj83off/job_working_directory/000/15/outputs/dataset_de499407-bd0d-4497-a7ae-58bd962252d3.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/a/a/0/dataset_aa06559a-c31e-4f53-9ca1-50c7b65e2a6a.dat -c /tmp/tmpvtvmbj0m/files/6/0/7/dataset_6076d2d8-04ad-454f-b0d1-b44203c217ae.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/15/outputs/dataset_8206c374-986e-4a2d-883d-826510572fd0.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/7/8/e/dataset_78e4da88-6bc8-43af-bfe6-8d37906fee0f.dat -c /tmp/tmpchj83off/files/5/3/5/dataset_535439dd-341d-4e21-9286-84aa079d5b25.dat -o /tmp/tmpchj83off/job_working_directory/000/15/outputs/dataset_de499407-bd0d-4497-a7ae-58bd962252d3.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam -#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/a/a/0/dataset_aa06559a-c31e-4f53-9ca1-50c7b65e2a6a.dat -c /tmp/tmpvtvmbj0m/files/6/0/7/dataset_6076d2d8-04ad-454f-b0d1-b44203c217ae.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/15/outputs/dataset_8206c374-986e-4a2d-883d-826510572fd0.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.0.3 +#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/7/8/e/dataset_78e4da88-6bc8-43af-bfe6-8d37906fee0f.dat -c /tmp/tmpchj83off/files/5/3/5/dataset_535439dd-341d-4e21-9286-84aa079d5b25.dat -o /tmp/tmpchj83off/job_working_directory/000/15/outputs/dataset_de499407-bd0d-4497-a7ae-58bd962252d3.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWI-ST560:29:B0A7LABXX:2:1101:5084:4188 ! 0 ! 0 - - NM HWI-ST560:29:B0A7LABXX:2:1101:5084:4188133chrI24200*=24200GGAACCGTAAAGGTTTATCGCGGTAGTAGTTTTTCACACGATTCGATAAA?<@DFDFD=FBHHCBHGGIJIIG:C@DGD??DDH?FHGHIJJDGCGEGG;AS:i:0XS:i:0Yt:Z:NM HWI-ST560:29:B0A7LABXX:2:1101:5084:418873chrI242009S41M=24200TTGATAGACTTCGTATGTGGAGTACTGTTTTATGGCGCTTATGTGTATTC11144222222322<<C<IHGHAEFCHEHHIHGCGHHHIIEGGGBB<<9?NM:i:0MD:Z:41AS:i:41XS:i:40XA:Z:chrXIV,-781623,50M,2;chrXI,+2426,50M,3;chrX,+9383,50M,3;chrIX,+9400,50M,3;Yt:Z:NM HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FHNM:i:0MD:Z:35AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15566:24141145chrI33506050M=3199-201TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCGHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_parsed_pairs_bam_min_mapq_40.pairs --- a/test-data/output_parsed_pairs_bam_min_mapq_40.pairs Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_parsed_pairs_bam_min_mapq_40.pairs Tue Apr 30 12:02:29 2024 +0000 |
| b |
| @@ -37,14 +37,14 @@ #samheader: @SQ SN:chrXV LN:1091291 #samheader: @SQ SN:chrXVI LN:948066 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/0/f/dataset_50f1299b-3b0f-4a0a-ae1e-e09b66e47369.dat -c /tmp/tmpvtvmbj0m/files/7/5/c/dataset_75c85deb-b408-42ff-90f5-5cea61a9594f.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/11/outputs/dataset_04ba0223-4885-4724-847b-02525a7ef606.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.0.3 +#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/0/b/d/dataset_0bd6cbee-0544-44c1-ad81-dd3845446ce7.dat -c /tmp/tmpchj83off/files/2/2/2/dataset_222eb307-af6a-471a-9d1d-00eab6969a45.dat -o /tmp/tmpchj83off/job_working_directory/000/11/outputs/dataset_55fc9726-73b7-4f53-83da-da08e1fbe4b9.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz -#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/0/f/dataset_50f1299b-3b0f-4a0a-ae1e-e09b66e47369.dat -c /tmp/tmpvtvmbj0m/files/7/5/c/dataset_75c85deb-b408-42ff-90f5-5cea61a9594f.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/11/outputs/dataset_04ba0223-4885-4724-847b-02525a7ef606.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/0/b/d/dataset_0bd6cbee-0544-44c1-ad81-dd3845446ce7.dat -c /tmp/tmpchj83off/files/2/2/2/dataset_222eb307-af6a-471a-9d1d-00eab6969a45.dat -o /tmp/tmpchj83off/job_working_directory/000/11/outputs/dataset_55fc9726-73b7-4f53-83da-da08e1fbe4b9.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/0/f/dataset_50f1299b-3b0f-4a0a-ae1e-e09b66e47369.dat -c /tmp/tmpvtvmbj0m/files/7/5/c/dataset_75c85deb-b408-42ff-90f5-5cea61a9594f.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/11/outputs/dataset_04ba0223-4885-4724-847b-02525a7ef606.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/0/b/d/dataset_0bd6cbee-0544-44c1-ad81-dd3845446ce7.dat -c /tmp/tmpchj83off/files/2/2/2/dataset_222eb307-af6a-471a-9d1d-00eab6969a45.dat -o /tmp/tmpchj83off/job_working_directory/000/11/outputs/dataset_55fc9726-73b7-4f53-83da-da08e1fbe4b9.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam -#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/0/f/dataset_50f1299b-3b0f-4a0a-ae1e-e09b66e47369.dat -c /tmp/tmpvtvmbj0m/files/7/5/c/dataset_75c85deb-b408-42ff-90f5-5cea61a9594f.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/11/outputs/dataset_04ba0223-4885-4724-847b-02525a7ef606.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.0.3 +#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/0/b/d/dataset_0bd6cbee-0544-44c1-ad81-dd3845446ce7.dat -c /tmp/tmpchj83off/files/2/2/2/dataset_222eb307-af6a-471a-9d1d-00eab6969a45.dat -o /tmp/tmpchj83off/job_working_directory/000/11/outputs/dataset_55fc9726-73b7-4f53-83da-da08e1fbe4b9.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWI-ST560:29:B0A7LABXX:2:1101:5084:4188 ! 0 ! 0 - - NM HWI-ST560:29:B0A7LABXX:2:1101:5084:4188133chrI24200*=24200GGAACCGTAAAGGTTTATCGCGGTAGTAGTTTTTCACACGATTCGATAAA?<@DFDFD=FBHHCBHGGIJIIG:C@DGD??DDH?FHGHIJJDGCGEGG;AS:i:0XS:i:0Yt:Z:NM HWI-ST560:29:B0A7LABXX:2:1101:5084:418873chrI242009S41M=24200TTGATAGACTTCGTATGTGGAGTACTGTTTTATGGCGCTTATGTGTATTC11144222222322<<C<IHGHAEFCHEHHIHGCGHHHIIEGGGBB<<9?NM:i:0MD:Z:41AS:i:41XS:i:40XA:Z:chrXIV,-781623,50M,2;chrXI,+2426,50M,3;chrX,+9383,50M,3;chrIX,+9400,50M,3;Yt:Z:NM HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FHNM:i:0MD:Z:35AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15566:24141145chrI33506050M=3199-201TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCGHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_parsed_pairs_bam_readid_dropped.pairs --- a/test-data/output_parsed_pairs_bam_readid_dropped.pairs Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_parsed_pairs_bam_readid_dropped.pairs Tue Apr 30 12:02:29 2024 +0000 |
| b |
| @@ -37,14 +37,14 @@ #samheader: @SQ SN:chrXV LN:1091291 #samheader: @SQ SN:chrXVI LN:948066 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/d/5/3/dataset_d53eccb1-028d-443e-aa5b-fb883976b07e.dat -c /tmp/tmpvtvmbj0m/files/d/c/c/dataset_dcc72f04-07a7-4159-8ecd-c8b978775fa1.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/19/outputs/dataset_86720212-8079-41ce-a66f-37e5222dc3ff.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.0.3 +#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/2/b/6/dataset_2b603561-f23a-44dd-92b4-9db918b88c03.dat -c /tmp/tmpchj83off/files/1/b/6/dataset_1b6c0c8f-df3e-40c0-9161-19d29b52573a.dat -o /tmp/tmpchj83off/job_working_directory/000/19/outputs/dataset_272af137-1fda-4769-b54c-23281e79fcd4.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz -#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/d/5/3/dataset_d53eccb1-028d-443e-aa5b-fb883976b07e.dat -c /tmp/tmpvtvmbj0m/files/d/c/c/dataset_dcc72f04-07a7-4159-8ecd-c8b978775fa1.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/19/outputs/dataset_86720212-8079-41ce-a66f-37e5222dc3ff.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/2/b/6/dataset_2b603561-f23a-44dd-92b4-9db918b88c03.dat -c /tmp/tmpchj83off/files/1/b/6/dataset_1b6c0c8f-df3e-40c0-9161-19d29b52573a.dat -o /tmp/tmpchj83off/job_working_directory/000/19/outputs/dataset_272af137-1fda-4769-b54c-23281e79fcd4.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/d/5/3/dataset_d53eccb1-028d-443e-aa5b-fb883976b07e.dat -c /tmp/tmpvtvmbj0m/files/d/c/c/dataset_dcc72f04-07a7-4159-8ecd-c8b978775fa1.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/19/outputs/dataset_86720212-8079-41ce-a66f-37e5222dc3ff.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/2/b/6/dataset_2b603561-f23a-44dd-92b4-9db918b88c03.dat -c /tmp/tmpchj83off/files/1/b/6/dataset_1b6c0c8f-df3e-40c0-9161-19d29b52573a.dat -o /tmp/tmpchj83off/job_working_directory/000/19/outputs/dataset_272af137-1fda-4769-b54c-23281e79fcd4.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam -#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/d/5/3/dataset_d53eccb1-028d-443e-aa5b-fb883976b07e.dat -c /tmp/tmpvtvmbj0m/files/d/c/c/dataset_dcc72f04-07a7-4159-8ecd-c8b978775fa1.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/19/outputs/dataset_86720212-8079-41ce-a66f-37e5222dc3ff.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.0.3 +#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/2/b/6/dataset_2b603561-f23a-44dd-92b4-9db918b88c03.dat -c /tmp/tmpchj83off/files/1/b/6/dataset_1b6c0c8f-df3e-40c0-9161-19d29b52573a.dat -o /tmp/tmpchj83off/job_working_directory/000/19/outputs/dataset_272af137-1fda-4769-b54c-23281e79fcd4.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 . ! 0 ! 0 - - NM HWI-ST560:29:B0A7LABXX:2:1101:5084:4188133chrI24200*=24200GGAACCGTAAAGGTTTATCGCGGTAGTAGTTTTTCACACGATTCGATAAA?<@DFDFD=FBHHCBHGGIJIIG:C@DGD??DDH?FHGHIJJDGCGEGG;AS:i:0XS:i:0Yt:Z:NM HWI-ST560:29:B0A7LABXX:2:1101:5084:418873chrI242009S41M=24200TTGATAGACTTCGTATGTGGAGTACTGTTTTATGGCGCTTATGTGTATTC11144222222322<<C<IHGHAEFCHEHHIHGCGHHHIIEGGGBB<<9?NM:i:0MD:Z:41AS:i:41XS:i:40XA:Z:chrXIV,-781623,50M,2;chrXI,+2426,50M,3;chrX,+9383,50M,3;chrIX,+9400,50M,3;Yt:Z:NM . chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FHNM:i:0MD:Z:35AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15566:24141145chrI33506050M=3199-201TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCGHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_parsed_pairs_bam_readid_dropped_seq.pairs --- a/test-data/output_parsed_pairs_bam_readid_dropped_seq.pairs Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_parsed_pairs_bam_readid_dropped_seq.pairs Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -4,13 +4,13 @@\n #chromsize: Test_seq 450060\n #samheader: @SQ\tSN:Test_seq\tLN:450060\n #samheader: @PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SP -T0 -t 8 test test_hic_reads_1.fq test_hic_reads_2.fq\n-#samheader: @PG\tID:pairtools_parse\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/6/d/e/dataset_6dee055e-91e3-4fb7-a2cb-65bb836b6b46.dat -c /tmp/tmpvtvmbj0m/files/f/6/d/dataset_f6d93a5f-aa4c-4b78-802c-e7b94fcee3e4.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/22/outputs/dataset_6d40908c-8b00-4098-8c50-3c42836de0ee.dat --min-mapq 40 --max-molecule-size 750 --drop-seq --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-mem2\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_parse\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/7/b/dataset_b7b0c820-0d14-4f18-95e3-c6fb58aae265.dat -c /tmp/tmpchj83off/files/d/7/1/dataset_d718e69b-ffe9-4c9d-ab83-1d209e3a56bf.dat -o /tmp/tmpchj83off/job_working_directory/000/22/outputs/dataset_e94790d6-3c0a-4eaf-a7ee-9cab4494c297.dat --min-mapq 40 --max-molecule-size 750 --drop-seq --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-mem2\tVN:1.1.0\n #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2\n A00126:224:H7HMWDSX3:3:1101:4779:3098\t!\t0\tTest_seq\t166211\t-\t-\tMU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19177\x19Test_seq\x19214824\x195\x1978M\x19=\x19166134\x19-48691\x19*\x19*\x19NM:i:3\x19MD:Z:1T33G33A8\x19MC:Z:78M\x19AS:i:66\x19XS:i:63\x19XA:Z:Test_seq,+166134,78M,3;\x19Yt:Z:MU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19113\x19Test_seq\x19166134\x1943\x1978M\x19=\x19214824\x1948691\x19*\x19*\x19NM:i:0\x19MD:Z:78\x19MC:Z:78M\x19AS:i:78\x19XS:i:63\x19XA:Z:Test_seq,+214829,5S73M,2;\x19Yt:Z:MU\n A00126:224:H7HMWDSX3:3:1101:2908:3239\t!\t0\tTest_seq\t167696\t-\t-\tMU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x19161\x19Test_seq\x19167331\x1923\x19151M\x19=\x19167546\x19366\x19*\x19*\x19NM:i:1\x19MD:Z:37A113\x19MC:Z:151M\x19AS:i:146\x19XS:i:135\x19XA:Z:Test_seq,-213553,151M,4;\x19Yt:Z:MU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x1981\x19Test_seq\x19167546\x1944\x19151M\x19=\x19167331\x19-366\x19*\x19*\x19NM:i:3\x19MD:Z:82G15T30C21\x19MC:Z:151M\x19AS:i:136\x19XS:i:114\x19XA:Z:Test_seq,+213342,118M2I23M2I6M,8;\x19Yt:Z:MU\n A00126:224:H7HMWDSX3:3:1101:27208:4492\tTest_seq\t194620\tTest_seq\t194909\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x1997\x19Test_seq\x19194620\x1960\x19151M\x19=\x19194778\x19290\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:132M19S\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x19145\x19Test_seq\x19194778\x1960\x19132M19S\x19=\x19194620\x19-290\x19*\x19*\x19NM:i:0\x19MD:Z:132\x19MC:Z:151M\x19AS:i:132\x19XS:i:0\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1101:9344:5306\t!\t0\t!\t0\t-\t-\tMM\tA00126:224:H7HMWDSX3:3:1101:9344:5306\x1997\x19Test_seq\x19449503\x197\x1960M\x19=\x19449503\x1960\x19*\x19*\x19NM:i:4\x19MD:Z:3T44G2C5G2\x19MC:Z:60M\x19AS:i:44\x19XS:i:40\x19XA:Z:Test_seq,+16926,60M,5;\x19Yt:Z:MM\tA00126:224:H7HMWDSX3:3:1101:9344:5306\x19145\x19Test_seq\x19449503\x1912\x1960M\x19=\x19449503\x19-60\x19*\x19*\x19NM:i:1\x19MD:Z:53T6\x19MC:Z:60M\x19AS:i:55\x19XS:i:50\x19XA:Z:Test_seq,-16926,60M,2;\x19Yt:Z:MM\n-A00126:224:H7HMWDSX3:3:1101:17607:5212\tTest_seq\t83425\tTest_seq\t93852\t-\t+\tUR\tA00126:224:H7HMWDSX3:3:1101:17607:5212\x1981\x19Test_seq\x1983397\x1960\x19122S29M\x19=\x1993852\x1910428\x19*\x19*\x19NM:i:0\x19MD:Z:29\x19MC:Z:151M\x19AS:i:29\x19XS:i:0\x19SA:Z:Test_seq,94155,-,122M29S,60,0;\x19Yt:Z:UR\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1101:17607:5212\x192129\x19Test_seq\x1994155\x1960\x19122M29H\x19=\x1993852\x19-425\x19*\x19*\x19NM:i:0\x19MD:Z:122\x19MC:Z:151M\x19AS:i:122\x19XS:i:0\x19SA:Z:Test_seq,83397,-,122S29M,60,0;\x19Yt:Z:UR\tA00126:224:H7HMWDSX3:3:1101:17607:5212\x19161\x19Test_seq\x1993852\x1960\x19151M\x19=\x1983397\x19-10428\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:122S29M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UR\n+A00126:224:H7HMWDSX3:3:1101:17607:5212\tTest_seq\t83425\tTest_seq\t93852\t-\t+\tUR\tA00126:224:H7HMWDSX3:3:1101:17607:5212\x192129\x19Test_seq\x1994155\x1960\x19122M29H\x19=\x1993852\x19-425\x19*\x19*\x19NM:i:0\x19MD:Z:122\x19MC:Z:151M\x19AS:i:122\x19XS:i:0\x19SA:Z:Test_seq,83397,-,122S29M,60,0;\x19Yt:Z:UR\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1101:17607:5212\x1981\x19Test_seq\x1983397\x1960\x19122S29M\x19=\x1993852\x1910428\x19*\x19*\x19NM:i:0\x19MD:Z:29\x19MC:Z:151M\x19AS:i:29\x19XS:i:0\x19SA:Z:Test_seq,94155,-,122M29S,60,0;\x19Yt:Z:UR\tA00126:224:H7HMWDSX3:3:1101:17607:5212\x19161\x19Test_seq\x1993852\x1960\x19151M\x19=\x1983397\x19-10428\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:122S29M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UR\n A00126:224:H7HMWDSX3:3:1101:17942:'..b'3:1115:15944:29731\t!\t0\tTest_seq\t167319\t-\t-\tMU\tA00126:224:H7HMWDSX3:3:1115:15944:29731\x1997\x19Test_seq\x19166867\x1938\x19151M\x19=\x19167169\x19453\x19*\x19*\x19NM:i:5\x19MD:Z:26G9G13T10A8T80\x19MC:Z:151M\x19AS:i:126\x19XS:i:106\x19XA:Z:Test_seq,-214017,151M,9;\x19Yt:Z:MU\tA00126:224:H7HMWDSX3:3:1115:15944:29731\x19145\x19Test_seq\x19167169\x1952\x19151M\x19=\x19166867\x19-453\x19*\x19*\x19NM:i:1\x19MD:Z:74T76\x19MC:Z:151M\x19AS:i:146\x19XS:i:121\x19XA:Z:Test_seq,+213715,151M,6;\x19Yt:Z:MU\n@@ -590,7 +590,7 @@\n A00126:224:H7HMWDSX3:3:1116:21097:1329\t!\t0\t!\t0\t-\t-\tMM\tA00126:224:H7HMWDSX3:3:1116:21097:1329\x1965\x19Test_seq\x19167966\x1921\x19151M\x19=\x19212718\x1944753\x19*\x19*\x19NM:i:11\x19MD:Z:7T4G3G2A35T29G8C34G0C4T3A11\x19MC:Z:151M\x19AS:i:96\x19XS:i:83\x19XA:Z:Test_seq,-212922,151M,14;\x19Yt:Z:MM\tA00126:224:H7HMWDSX3:3:1116:21097:1329\x19129\x19Test_seq\x19212718\x1931\x19151M\x19=\x19167966\x19-44753\x19*\x19*\x19NM:i:1\x19MD:Z:108A42\x19MC:Z:151M\x19AS:i:146\x19XS:i:131\x19XA:Z:Test_seq,-168170,151M,4;\x19Yt:Z:MM\n A00126:224:H7HMWDSX3:3:1116:9525:1548\tTest_seq\t165792\tTest_seq\t166199\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:9525:1548\x19161\x19Test_seq\x19165792\x1960\x19110M2D41M\x19=\x19166049\x19408\x19*\x19*\x19NM:i:12\x19MD:Z:2A5T9T13C31A10A8G11A13^CC7G19T13\x19MC:Z:151M\x19AS:i:95\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:9525:1548\x1981\x19Test_seq\x19166049\x1960\x19151M\x19=\x19165792\x19-408\x19*\x19*\x19NM:i:1\x19MD:Z:53G97\x19MC:Z:110M2D41M\x19AS:i:146\x19XS:i:50\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1116:28917:2190\tTest_seq\t74270\tTest_seq\t74579\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:28917:2190\x1997\x19Test_seq\x1974270\x1960\x19151M\x19=\x1974429\x19310\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:151M\x19AS:i:151\x19XS:i:41\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:28917:2190\x19145\x19Test_seq\x1974429\x1960\x19151M\x19=\x1974270\x19-310\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:151M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\n-A00126:224:H7HMWDSX3:3:1116:3495:3724\tTest_seq\t335700\tTest_seq\t436771\t-\t-\tUR\tA00126:224:H7HMWDSX3:3:1116:3495:3724\x19177\x19Test_seq\x19335669\x1960\x19119S32M\x19=\x19436621\x19101072\x19*\x19*\x19NM:i:0\x19MD:Z:32\x19MC:Z:151M\x19AS:i:32\x19XS:i:0\x19SA:Z:Test_seq,436401,+,32S119M,60,0;\x19Yt:Z:UR\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1116:3495:3724\x192209\x19Test_seq\x19436401\x1960\x1932H119M\x19=\x19436621\x19371\x19*\x19*\x19NM:i:0\x19MD:Z:119\x19MC:Z:151M\x19AS:i:119\x19XS:i:0\x19SA:Z:Test_seq,335669,-,119S32M,60,0;\x19Yt:Z:UR\tA00126:224:H7HMWDSX3:3:1116:3495:3724\x19113\x19Test_seq\x19436621\x1960\x19151M\x19=\x19335669\x19-101072\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:119S32M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UR\n+A00126:224:H7HMWDSX3:3:1116:3495:3724\tTest_seq\t335700\tTest_seq\t436771\t-\t-\tUR\tA00126:224:H7HMWDSX3:3:1116:3495:3724\x192209\x19Test_seq\x19436401\x1960\x1932H119M\x19=\x19436621\x19371\x19*\x19*\x19NM:i:0\x19MD:Z:119\x19MC:Z:151M\x19AS:i:119\x19XS:i:0\x19SA:Z:Test_seq,335669,-,119S32M,60,0;\x19Yt:Z:UR\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1116:3495:3724\x19177\x19Test_seq\x19335669\x1960\x19119S32M\x19=\x19436621\x19101072\x19*\x19*\x19NM:i:0\x19MD:Z:32\x19MC:Z:151M\x19AS:i:32\x19XS:i:0\x19SA:Z:Test_seq,436401,+,32S119M,60,0;\x19Yt:Z:UR\tA00126:224:H7HMWDSX3:3:1116:3495:3724\x19113\x19Test_seq\x19436621\x1960\x19151M\x19=\x19335669\x19-101072\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:119S32M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UR\n A00126:224:H7HMWDSX3:3:1116:1886:5885\tTest_seq\t133235\tTest_seq\t133657\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:1886:5885\x1997\x19Test_seq\x19133235\x1960\x19151M\x19=\x19133507\x19423\x19*\x19*\x19NM:i:1\x19MD:Z:36C114\x19MC:Z:151M\x19AS:i:146\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:1886:5885\x19145\x19Test_seq\x19133507\x1960\x19151M\x19=\x19133235\x19-423\x19*\x19*\x19NM:i:5\x19MD:Z:12G29T70C20C2C13\x19MC:Z:151M\x19AS:i:126\x19XS:i:0\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1116:5041:6715\tTest_seq\t168462\tTest_seq\t168810\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:5041:6715\x1997\x19Test_seq\x19168462\x1960\x19151M\x19=\x19168674\x19349\x19*\x19*\x19NM:i:1\x19MD:Z:33T117\x19MC:Z:137M14S\x19AS:i:146\x19XS:i:91\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:5041:6715\x19145\x19Test_seq\x19168674\x1960\x19137M14S\x19=\x19168462\x19-349\x19*\x19*\x19NM:i:5\x19MD:Z:42T10T2C7A19G52\x19MC:Z:151M\x19AS:i:112\x19XS:i:30\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1116:31720:7545\t!\t0\tTest_seq\t303522\t-\t+\tMR\tA00126:224:H7HMWDSX3:3:1116:31720:7545\x1965\x19Test_seq\x19305328\x196\x1920M131S\x19=\x19303522\x19-1807\x19*\x19*\x19NM:i:0\x19MD:Z:20\x19MC:Z:151M\x19AS:i:20\x19XS:i:0\x19SA:Z:Test_seq,303836,-,131M20S,60,0;\x19Yt:Z:MR\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1116:31720:7545\x192129\x19Test_seq\x19303836\x1960\x19131M20H\x19=\x19303522\x19-445\x19*\x19*\x19NM:i:0\x19MD:Z:131\x19MC:Z:151M\x19AS:i:131\x19XS:i:43\x19SA:Z:Test_seq,305328,+,20M131S,6,0;\x19Yt:Z:MR\tA00126:224:H7HMWDSX3:3:1116:31720:7545\x19129\x19Test_seq\x19303522\x1960\x19151M\x19=\x19305328\x191807\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:20M131S\x19AS:i:151\x19XS:i:0\x19Yt:Z:MR\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_parsed_pairs_sam.pairs --- a/test-data/output_parsed_pairs_sam.pairs Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_parsed_pairs_sam.pairs Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -4,13 +4,13 @@\n #chromsize: Test_seq 450060\n #samheader: @SQ\tSN:Test_seq\tLN:450060\n #samheader: @PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SP -T0 -t 8 test test_hic_reads_1.fq test_hic_reads_2.fq\n-#samheader: @PG\tID:pairtools_parse\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/1/f/1/dataset_1f1b27bb-444f-4f9a-b79d-0addfd198f84.dat -c /tmp/tmpvtvmbj0m/files/a/6/c/dataset_a6c25687-079e-4e5f-a858-96e64dab4aff.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/3/outputs/dataset_4f9f5c5c-4d65-4e66-9fd4-61c5ab9be509.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-mem2\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_parse\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/2/e/1/dataset_2e1a2abe-d4ed-46d7-90b0-02f7ad21e679.dat -c /tmp/tmpchj83off/files/4/0/d/dataset_40dde3ed-dc87-49a5-b6d7-c9bb448a57ee.dat -o /tmp/tmpchj83off/job_working_directory/000/3/outputs/dataset_bb5fe9ed-7777-4b2b-88c3-9f89a9d6e0ce.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-mem2\tVN:1.1.0\n #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2\n A00126:224:H7HMWDSX3:3:1101:4779:3098\tTest_seq\t166211\tTest_seq\t214901\t-\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19113\x19Test_seq\x19166134\x1943\x1978M\x19=\x19214824\x1948691\x19GGGCACCAACTAGTTCTTCTGGTCTCAGGATAATGTAGGTCTCTGGTTCATGTGGCCCTTTCTGTCTCTTGGGTTCTT\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:78\x19MC:Z:78M\x19AS:i:78\x19XS:i:63\x19XA:Z:Test_seq,+214829,5S73M,2;\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19177\x19Test_seq\x19214824\x195\x1978M\x19=\x19166134\x19-48691\x19AAGAGCCCAAGAGACAGAAAGGGCCACATGAACCACAGACCTACATCATCCTGAGACCAGAAGAACTAGTTGGTGCCC\x19FFFF,FFFFFFFFFFFFF,FFFFFFFFFFFF:FF:,FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF\x19NM:i:3\x19MD:Z:1T33G33A8\x19MC:Z:78M\x19AS:i:66\x19XS:i:63\x19XA:Z:Test_seq,+166134,78M,3;\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1101:2908:3239\tTest_seq\t167331\tTest_seq\t167696\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x19161\x19Test_seq\x19167331\x1923\x19151M\x19=\x19167546\x19366\x19TGAGATGTCATAGCTGAATATTCTTTCCCAGTCTGTAGGTGGTCTTTTTACTCTTTTGGTGAAGTCTTTAGATGAGCATAGGTGTTTGATTTTTAGGAGCTCCCAGTTATCTGGTTTCTCTTCATCATTTTTGGTAATGTTTTGTATTCTG\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFF:FFFFF:FFFF:FFFFFFFFFFFFFFF:FF,,FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF:FFFFFFFF:FF,FF\x19NM:i:1\x19MD:Z:37A113\x19MC:Z:151M\x19AS:i:146\x19XS:i:135\x19XA:Z:Test_seq,-213553,151M,4;\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x1981\x19Test_seq\x19167546\x1944\x19151M\x19=\x19167331\x19-366\x19TAGTCTTTATGTTTAGGTCTTTGATCCACTTGGAGTTAGTTTTTGTGCATGGTGTGAGGTATGGGTCCTGTTTCATTCTTTTACAAATGGATATCCAGGTATGCCAGCACCATTTGTTAAAAAGACTATTATTTCCCCAATTGACTGACAC\x19FF,F,F:FFFFFFFFF,FFF:FFFFFF:FFFF:FFFFFFFFFFF:FF::F,FFFFFFFFF:,F,FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FFF::FFFFFFFFFFFFF,FFFFFFF:FF:F,:FFFFFFFFFF,F,F:FFFFFFFFFF\x19NM:i:3\x19MD:Z:82G15T30C21\x19MC:Z:151M\x19AS:i:136\x19XS:i:114\x19XA:Z:Test_seq,+213342,118M2I23M2I6M,8;\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1101:27208:4492\tTest_seq\t194620\tTest_seq\t194909\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x1997\x19Test_seq\x19194620\x1960\x19151M\x19=\x19194778\x19290\x19GCTGTGCAAACCACTGCTCCAGGCTATCTCAGCACTGAGCCAGAGACAAGGGCCAGTTCAGTCACCTGGAAAATCAGGCCAGCATCTCTGAAAAATAGGTGCCTCAGTGTTCACAGAAAAGGGCCATGTATTGAAGTAGGTCAGAGGAAGA\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:F,FF:::FFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:151\x19MC:Z:132M19S\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x19145\x19Test_seq\x19194778\x1960\x19132M19S\x19=\x19194620\x19-290\x19CACTCACCAGATTCAGCCCAGGACCAGAGGCTGCCGAGGGCAGGTGTGGGACGAAGTCAAGATGAAGTCAGTTCATTGTGTGGTTTTCGGTACCAGGCTAGACCTAGATTTGAACCCCAAGTCTGCTACTTAGATCATTCATTCAATGTGT\x19FFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:132\x19MC:Z:151M\x19AS:i:132\x19XS:i:0\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1101:9344:5306\tTest_se'..b':FFFF,FFF:FFF:FF:F,FFF:FFFFFFF:FFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:32\x19MC:Z:151M\x19AS:i:32\x19XS:i:0\x19SA:Z:Test_seq,436401,+,32S119M,60,0;\x19Yt:Z:UR\tA00126:224:H7HMWDSX3:3:1116:3495:3724\x19113\x19Test_seq\x19436621\x1960\x19151M\x19=\x19335669\x19-101072\x19AAAAATGCCACGTTGGATTAACCTTGACTCAACTGGACATGTAGATACCCCATGTGGATGGTTAGAGGGGTGGCAAGGTCCATCCTCCCCAAAGAGACTGTATCCCTACCTGCCCGAGGACCTGAAGTGGTTACGTGTCCAACCAGTTGCC\x19FFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFF\x19NM:i:0\x19MD:Z:151\x19MC:Z:119S32M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UR\n A00126:224:H7HMWDSX3:3:1116:1886:5885\tTest_seq\t133235\tTest_seq\t133657\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:1886:5885\x1997\x19Test_seq\x19133235\x1960\x19151M\x19=\x19133507\x19423\x19AATCATGGTCCAGCCAAGTTGGCACATAAGGTTAACAATCATAGCCAGCGTTACTCTTGCCTTGCACCTCGGTGTTCGTTACTGCCAGATGTACGTCGTTAATGTGCGTAACAGTCAGATACGAGATTTTTTACTATTGTCATGAACGTAA\x19FFFFFFF:FFFF,FFFFFFF,FFFFF:FF,FFFF::,FFFFFFFFFF,F:FFFFFFFFF,FFFFFF,FFF,FFFFFF,FFFFF,FFFFFFFFFF:FFFFFFFFFF:::FFF,FFF:F,FFFF,F:FFFFFF:F,FFFF,F,FF::F,FFFF\x19NM:i:1\x19MD:Z:36C114\x19MC:Z:151M\x19AS:i:146\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:1886:5885\x19145\x19Test_seq\x19133507\x1960\x19151M\x19=\x19133235\x19-423\x19GGGGTTTCACTGTCTGGTTTTTAGAAGCAGCATGCCAGGTCTCTGTTCCCTAGTCCACCTTAGTCTGGACACTCCGCTGAAACCTGTCCAGTGTCATAGCGACACACAGGCCTACACTGAGAGACAAGTGGTGGATGAATTTGAAGTACGT\x19:F::FFFFFFFF,FF,FFF,,F:FFF,FFFFFF,FFF,:F:F::FFFF,FFF:F,:FFFFFFFF:,,F,:FF:FFFFFFFFFFFFFF:FFFF:F:FFFFF::FFFFFFFFF,F,FFFFFFFFFF,FFFFFFFFF,FF,F:FFFFFFFFF,F\x19NM:i:5\x19MD:Z:12G29T70C20C2C13\x19MC:Z:151M\x19AS:i:126\x19XS:i:0\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1116:5041:6715\tTest_seq\t168462\tTest_seq\t168810\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:5041:6715\x1997\x19Test_seq\x19168462\x1960\x19151M\x19=\x19168674\x19349\x19GAGCGGTGATAAAGGGCATCCTTGTCTGGTTCCCGTTCTCAAGGGAAATGCTTTCAGGTTCTCTCCATTTAGAGTGATATTGGCTGTTGGCTTTGCATAGATGCCCTTTATTATGTTGAGGAATTTTCCTTCAATTCCTATTTTGGTAAGA\x19FFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFF::F:F:F,FFFFFFFFFFFF:F:F:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,FFF:FFFFFF:FF:FFFF,FFFFFFFF:FFF,F:,FFFFF:FFF\x19NM:i:1\x19MD:Z:33T117\x19MC:Z:137M14S\x19AS:i:146\x19XS:i:91\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:5041:6715\x19145\x19Test_seq\x19168674\x1960\x19137M14S\x19=\x19168462\x19-349\x19TCATGTGGTTTTTATCTTTTGTTTTATTTATGTGATGGATTACATTAATGGTTCTTTTGATATTGAACCAGCCTTGCATACCTGATATAAATCCCACTTGATCAGGGTGAATTATTTTTTTGATGTGTTGTTGGATTGATCTCCGGGACTT\x19F:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:F:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\x19NM:i:5\x19MD:Z:42T10T2C7A19G52\x19MC:Z:151M\x19AS:i:112\x19XS:i:30\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1116:31720:7545\tTest_seq\t303522\tTest_seq\t305328\t+\t+\tRU\tA00126:224:H7HMWDSX3:3:1116:31720:7545\x19129\x19Test_seq\x19303522\x1960\x19151M\x19=\x19305328\x191807\x19ATCTTTTATTTGGGAGAAACAAGTCAGAATTAATTCCTGTTGATTGCACTGAATTATAAATGATGAAGAATCAGAAATCAGCTACTGGCCCACAGGCATGTTGCAGAAACTCAATAAATGTTAGCCATCATCTCCTTTTTCATCATCATAA\x19FFFFFFF:FFFF:F:FFFFFFFFFF:FFF:FFFF:FFFF,FFFFFFFFF,FFFFF::FFF:FFFFFFFFFFFFFFF,F:FFFFFFFFFF:FF:FF:FFFF,FFF:FFF:FFFFFF:FFFFFF,F:F,FFFFF:FFF:FFF:FFFF,FFF:F\x19NM:i:0\x19MD:Z:151\x19MC:Z:20M131S\x19AS:i:151\x19XS:i:0\x19Yt:Z:RU\tA00126:224:H7HMWDSX3:3:1116:31720:7545\x1965\x19Test_seq\x19305328\x196\x1920M131S\x19=\x19303522\x19-1807\x19CCATTGCTATCAAGTGGATTGATCACTCCCTGGAGAAGGACATCATGCTTGGTAAAGTAGAGGGCCAACATGGATTGACACAGTGGCTGCAACAATGGGCTCAAGCATAACAACAACTGTGAGGATGGCGCAGGGCTGGGCAGTGTTTCAT\x19FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFF:FF:FFF:FFFFF:F:FFFFFFFFF,F::FFFFFF:FFFFFFFFFFFFFFF,F:FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:20\x19MC:Z:151M\x19AS:i:20\x19XS:i:0\x19SA:Z:Test_seq,303836,-,131M20S,60,0;\x19Yt:Z:RU\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1116:31720:7545\x192129\x19Test_seq\x19303836\x1960\x19131M20H\x19=\x19303522\x19-445\x19ATGAAACACTGCCCAGCCCTGCGCCATCCTCACAGTTGTTGTTATGCTTGAGCCCATTGTTGCAGCCACTGTGTCAATCCATGTTGGCCCTCTACTTTACCAAGCATGATGTCCTTCTCCAGGGAGTGATC\x19FFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:F,FFFFFFFFFFFFFFF:FFFFFF::F,FFFFFFFFF:F:FFFFF:FFF:FF:FFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:131\x19MC:Z:151M\x19AS:i:131\x19XS:i:43\x19SA:Z:Test_seq,305328,+,20M131S,6,0;\x19Yt:Z:RU\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_parsed_pairs_sam_assemblyname.pairs --- a/test-data/output_parsed_pairs_sam_assemblyname.pairs Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_parsed_pairs_sam_assemblyname.pairs Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -4,13 +4,13 @@\n #chromsize: Test_seq 450060\n #samheader: @SQ\tSN:Test_seq\tLN:450060\n #samheader: @PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SP -T0 -t 8 test test_hic_reads_1.fq test_hic_reads_2.fq\n-#samheader: @PG\tID:pairtools_parse\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpqgxtfoa0/files/1/0/c/dataset_10cd8bd7-2817-493f-9564-e4ab0fd42e68.dat -c /tmp/tmpqgxtfoa0/files/a/b/0/dataset_ab072667-6807-4c7f-9c2f-4a8de9dd1caa.dat --assembly test_assembly -o /tmp/tmpqgxtfoa0/job_working_directory/000/28/outputs/dataset_a8df527f-2db8-468b-a5eb-bd15b7e24367.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-mem2\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_parse\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/5/2/e/dataset_52effa56-a42c-41a9-802e-401d7a5813de.dat -c /tmp/tmpchj83off/files/8/d/d/dataset_8dd0a91e-ecbd-4f98-86cd-2510709cac82.dat --assembly test_assembly -o /tmp/tmpchj83off/job_working_directory/000/28/outputs/dataset_0a87c13d-5811-4e81-9626-bb8665d07df4.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-mem2\tVN:1.1.0\n #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2\n A00126:224:H7HMWDSX3:3:1101:4779:3098\tTest_seq\t166211\tTest_seq\t214901\t-\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19113\x19Test_seq\x19166134\x1943\x1978M\x19=\x19214824\x1948691\x19GGGCACCAACTAGTTCTTCTGGTCTCAGGATAATGTAGGTCTCTGGTTCATGTGGCCCTTTCTGTCTCTTGGGTTCTT\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:78\x19MC:Z:78M\x19AS:i:78\x19XS:i:63\x19XA:Z:Test_seq,+214829,5S73M,2;\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19177\x19Test_seq\x19214824\x195\x1978M\x19=\x19166134\x19-48691\x19AAGAGCCCAAGAGACAGAAAGGGCCACATGAACCACAGACCTACATCATCCTGAGACCAGAAGAACTAGTTGGTGCCC\x19FFFF,FFFFFFFFFFFFF,FFFFFFFFFFFF:FF:,FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF\x19NM:i:3\x19MD:Z:1T33G33A8\x19MC:Z:78M\x19AS:i:66\x19XS:i:63\x19XA:Z:Test_seq,+166134,78M,3;\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1101:2908:3239\tTest_seq\t167331\tTest_seq\t167696\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x19161\x19Test_seq\x19167331\x1923\x19151M\x19=\x19167546\x19366\x19TGAGATGTCATAGCTGAATATTCTTTCCCAGTCTGTAGGTGGTCTTTTTACTCTTTTGGTGAAGTCTTTAGATGAGCATAGGTGTTTGATTTTTAGGAGCTCCCAGTTATCTGGTTTCTCTTCATCATTTTTGGTAATGTTTTGTATTCTG\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFF:FFFFF:FFFF:FFFFFFFFFFFFFFF:FF,,FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF:FFFFFFFF:FF,FF\x19NM:i:1\x19MD:Z:37A113\x19MC:Z:151M\x19AS:i:146\x19XS:i:135\x19XA:Z:Test_seq,-213553,151M,4;\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x1981\x19Test_seq\x19167546\x1944\x19151M\x19=\x19167331\x19-366\x19TAGTCTTTATGTTTAGGTCTTTGATCCACTTGGAGTTAGTTTTTGTGCATGGTGTGAGGTATGGGTCCTGTTTCATTCTTTTACAAATGGATATCCAGGTATGCCAGCACCATTTGTTAAAAAGACTATTATTTCCCCAATTGACTGACAC\x19FF,F,F:FFFFFFFFF,FFF:FFFFFF:FFFF:FFFFFFFFFFF:FF::F,FFFFFFFFF:,F,FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FFF::FFFFFFFFFFFFF,FFFFFFF:FF:F,:FFFFFFFFFF,F,F:FFFFFFFFFF\x19NM:i:3\x19MD:Z:82G15T30C21\x19MC:Z:151M\x19AS:i:136\x19XS:i:114\x19XA:Z:Test_seq,+213342,118M2I23M2I6M,8;\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1101:27208:4492\tTest_seq\t194620\tTest_seq\t194909\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x1997\x19Test_seq\x19194620\x1960\x19151M\x19=\x19194778\x19290\x19GCTGTGCAAACCACTGCTCCAGGCTATCTCAGCACTGAGCCAGAGACAAGGGCCAGTTCAGTCACCTGGAAAATCAGGCCAGCATCTCTGAAAAATAGGTGCCTCAGTGTTCACAGAAAAGGGCCATGTATTGAAGTAGGTCAGAGGAAGA\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:F,FF:::FFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:151\x19MC:Z:132M19S\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x19145\x19Test_seq\x19194778\x1960\x19132M19S\x19=\x19194620\x19-290\x19CACTCACCAGATTCAGCCCAGGACCAGAGGCTGCCGAGGGCAGGTGTGGGACGAAGTCAAGATGAAGTCAGTTCATTGTGTGGTTTTCGGTACCAGGCTAGACCTAGATTTGAACCCCAAGTCTGCTACTTAGATCATTCATTCAATGTGT\x19FFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:132\x19MC:Z:151M\x19AS:i:132\x19XS:i:0\x19Yt'..b':FFFF,FFF:FFF:FF:F,FFF:FFFFFFF:FFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:32\x19MC:Z:151M\x19AS:i:32\x19XS:i:0\x19SA:Z:Test_seq,436401,+,32S119M,60,0;\x19Yt:Z:UR\tA00126:224:H7HMWDSX3:3:1116:3495:3724\x19113\x19Test_seq\x19436621\x1960\x19151M\x19=\x19335669\x19-101072\x19AAAAATGCCACGTTGGATTAACCTTGACTCAACTGGACATGTAGATACCCCATGTGGATGGTTAGAGGGGTGGCAAGGTCCATCCTCCCCAAAGAGACTGTATCCCTACCTGCCCGAGGACCTGAAGTGGTTACGTGTCCAACCAGTTGCC\x19FFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFF\x19NM:i:0\x19MD:Z:151\x19MC:Z:119S32M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UR\n A00126:224:H7HMWDSX3:3:1116:1886:5885\tTest_seq\t133235\tTest_seq\t133657\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:1886:5885\x1997\x19Test_seq\x19133235\x1960\x19151M\x19=\x19133507\x19423\x19AATCATGGTCCAGCCAAGTTGGCACATAAGGTTAACAATCATAGCCAGCGTTACTCTTGCCTTGCACCTCGGTGTTCGTTACTGCCAGATGTACGTCGTTAATGTGCGTAACAGTCAGATACGAGATTTTTTACTATTGTCATGAACGTAA\x19FFFFFFF:FFFF,FFFFFFF,FFFFF:FF,FFFF::,FFFFFFFFFF,F:FFFFFFFFF,FFFFFF,FFF,FFFFFF,FFFFF,FFFFFFFFFF:FFFFFFFFFF:::FFF,FFF:F,FFFF,F:FFFFFF:F,FFFF,F,FF::F,FFFF\x19NM:i:1\x19MD:Z:36C114\x19MC:Z:151M\x19AS:i:146\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:1886:5885\x19145\x19Test_seq\x19133507\x1960\x19151M\x19=\x19133235\x19-423\x19GGGGTTTCACTGTCTGGTTTTTAGAAGCAGCATGCCAGGTCTCTGTTCCCTAGTCCACCTTAGTCTGGACACTCCGCTGAAACCTGTCCAGTGTCATAGCGACACACAGGCCTACACTGAGAGACAAGTGGTGGATGAATTTGAAGTACGT\x19:F::FFFFFFFF,FF,FFF,,F:FFF,FFFFFF,FFF,:F:F::FFFF,FFF:F,:FFFFFFFF:,,F,:FF:FFFFFFFFFFFFFF:FFFF:F:FFFFF::FFFFFFFFF,F,FFFFFFFFFF,FFFFFFFFF,FF,F:FFFFFFFFF,F\x19NM:i:5\x19MD:Z:12G29T70C20C2C13\x19MC:Z:151M\x19AS:i:126\x19XS:i:0\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1116:5041:6715\tTest_seq\t168462\tTest_seq\t168810\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:5041:6715\x1997\x19Test_seq\x19168462\x1960\x19151M\x19=\x19168674\x19349\x19GAGCGGTGATAAAGGGCATCCTTGTCTGGTTCCCGTTCTCAAGGGAAATGCTTTCAGGTTCTCTCCATTTAGAGTGATATTGGCTGTTGGCTTTGCATAGATGCCCTTTATTATGTTGAGGAATTTTCCTTCAATTCCTATTTTGGTAAGA\x19FFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFF::F:F:F,FFFFFFFFFFFF:F:F:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,FFF:FFFFFF:FF:FFFF,FFFFFFFF:FFF,F:,FFFFF:FFF\x19NM:i:1\x19MD:Z:33T117\x19MC:Z:137M14S\x19AS:i:146\x19XS:i:91\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:5041:6715\x19145\x19Test_seq\x19168674\x1960\x19137M14S\x19=\x19168462\x19-349\x19TCATGTGGTTTTTATCTTTTGTTTTATTTATGTGATGGATTACATTAATGGTTCTTTTGATATTGAACCAGCCTTGCATACCTGATATAAATCCCACTTGATCAGGGTGAATTATTTTTTTGATGTGTTGTTGGATTGATCTCCGGGACTT\x19F:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:F:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\x19NM:i:5\x19MD:Z:42T10T2C7A19G52\x19MC:Z:151M\x19AS:i:112\x19XS:i:30\x19Yt:Z:UU\n A00126:224:H7HMWDSX3:3:1116:31720:7545\tTest_seq\t303522\tTest_seq\t305328\t+\t+\tRU\tA00126:224:H7HMWDSX3:3:1116:31720:7545\x19129\x19Test_seq\x19303522\x1960\x19151M\x19=\x19305328\x191807\x19ATCTTTTATTTGGGAGAAACAAGTCAGAATTAATTCCTGTTGATTGCACTGAATTATAAATGATGAAGAATCAGAAATCAGCTACTGGCCCACAGGCATGTTGCAGAAACTCAATAAATGTTAGCCATCATCTCCTTTTTCATCATCATAA\x19FFFFFFF:FFFF:F:FFFFFFFFFF:FFF:FFFF:FFFF,FFFFFFFFF,FFFFF::FFF:FFFFFFFFFFFFFFF,F:FFFFFFFFFF:FF:FF:FFFF,FFF:FFF:FFFFFF:FFFFFF,F:F,FFFFF:FFF:FFF:FFFF,FFF:F\x19NM:i:0\x19MD:Z:151\x19MC:Z:20M131S\x19AS:i:151\x19XS:i:0\x19Yt:Z:RU\tA00126:224:H7HMWDSX3:3:1116:31720:7545\x1965\x19Test_seq\x19305328\x196\x1920M131S\x19=\x19303522\x19-1807\x19CCATTGCTATCAAGTGGATTGATCACTCCCTGGAGAAGGACATCATGCTTGGTAAAGTAGAGGGCCAACATGGATTGACACAGTGGCTGCAACAATGGGCTCAAGCATAACAACAACTGTGAGGATGGCGCAGGGCTGGGCAGTGTTTCAT\x19FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFF:FF:FFF:FFFFF:F:FFFFFFFFF,F::FFFFFF:FFFFFFFFFFFFFFF,F:FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:20\x19MC:Z:151M\x19AS:i:20\x19XS:i:0\x19SA:Z:Test_seq,303836,-,131M20S,60,0;\x19Yt:Z:RU\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1116:31720:7545\x192129\x19Test_seq\x19303836\x1960\x19131M20H\x19=\x19303522\x19-445\x19ATGAAACACTGCCCAGCCCTGCGCCATCCTCACAGTTGTTGTTATGCTTGAGCCCATTGTTGCAGCCACTGTGTCAATCCATGTTGGCCCTCTACTTTACCAAGCATGATGTCCTTCTCCAGGGAGTGATC\x19FFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:F,FFFFFFFFFFFFFFF:FFFFFF::F,FFFFFFFFF:F:FFFFF:FFF:FF:FFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:131\x19MC:Z:151M\x19AS:i:131\x19XS:i:43\x19SA:Z:Test_seq,305328,+,20M131S,6,0;\x19Yt:Z:RU\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/output_sorted_pairs.pairs --- a/test-data/output_sorted_pairs.pairs Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/output_sorted_pairs.pairs Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -38,18 +38,18 @@\n #samheader: @SQ\tSN:chrXV\tLN:1091291\n #samheader: @SQ\tSN:chrXVI\tLN:948066\n #samheader: @PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa\tVN:1.0.3\n-#samheader: @PG\tID:pairtools_sort-1.3\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/d/5/c/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/2/outputs/dataset_b446f275-b840-40de-9fb8-08bd13d19337.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-1.2\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-1.3\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/8/6/3/dataset_863ae21a-b207-4ba9-b94f-54406023b20a.dat -o /tmp/tmptyq9evah/job_working_directory/000/2/outputs/dataset_de1b3c74-45c1-408a-bb81-f91bacfb79cd.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-1.2\tVN:1.1.0\n #samheader: @PG\tID:bwa-2CCE5976\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-2CCE5976\tVN:1.0.3\n-#samheader: @PG\tID:pairtools_sort-2.3\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/d/5/c/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/2/outputs/dataset_b446f275-b840-40de-9fb8-08bd13d19337.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-2.2\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-2CCE5976\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-2.3\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/8/6/3/dataset_863ae21a-b207-4ba9-b94f-54406023b20a.dat -o /tmp/tmptyq9evah/job_working_directory/000/2/outputs/dataset_de1b3c74-45c1-408a-bb81-f91bacfb79cd.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-2.2\tVN:1.1.0\n #samheader: @PG\tID:bwa-3CAFD9D9\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92'..b'/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/2/outputs/dataset_b446f275-b840-40de-9fb8-08bd13d19337.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-3.2\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-3CAFD9D9\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-3.3\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/8/6/3/dataset_863ae21a-b207-4ba9-b94f-54406023b20a.dat -o /tmp/tmptyq9evah/job_working_directory/000/2/outputs/dataset_de1b3c74-45c1-408a-bb81-f91bacfb79cd.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-3.2\tVN:1.1.0\n #samheader: @PG\tID:bwa-4548A671\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz\n #samheader: @PG\tID:samtools\tPN:samtools\tPP:bwa-4548A671\tVN:1.19.2\tCL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam\n-#samheader: @PG\tID:pairtools_parse-4.3\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:samtools\tVN:1.0.3\n-#samheader: @PG\tID:pairtools_sort-4.4\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/d/5/c/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/2/outputs/dataset_b446f275-b840-40de-9fb8-08bd13d19337.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-4.3\tVN:1.0.3\n+#samheader: @PG\tID:pairtools_parse-4.3\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:samtools\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-4.4\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/8/6/3/dataset_863ae21a-b207-4ba9-b94f-54406023b20a.dat -o /tmp/tmptyq9evah/job_working_directory/000/2/outputs/dataset_de1b3c74-45c1-408a-bb81-f91bacfb79cd.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-4.3\tVN:1.1.0\n #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2\n HWUSI-EAS1533_0033_FC:1:1:1193:16038\t!\t0\t!\t0\t-\t-\tMM\tHWUSI-EAS1533_0033_FC:1:1:1193:16038\x1981\x19chrIV\x191529635\x190\x1936M\x19chrIX\x1918722\x190\x19AATTGACATTAAGCAATTGATGATGGTGATCATGCT\x19@@@@@@C@@C@C@@CCCCC@@CC@CC7777832324\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:36\x19Yt:Z:MM\tHWUSI-EAS1533_0033_FC:1:1:1193:16038\x19161\x19chrIX\x1918722\x190\x1936M\x19chrIV\x191529635\x190\x19NAAGTAAATTTACGATCTGGAAGGAGTGCTGTATGT\x19&,,,,22032@@@@@@@@@@@@@@@@@@@@@@@@@@\x19NM:i:2\x19MD:Z:0A11G23\x19AS:i:30\x19XS:i:30\x19XA:Z:chrX,+18705,36M,2;chrXV,+24474,36M,2;\x19Yt:Z:MM\n HWUSI-EAS1533_0033_FC:1:1:2292:14294\t!\t0\t!\t0\t-\t-\tMM\tHWUSI-EAS1533_0033_FC:1:1:2292:14294\x1981\x19chrVII\x191001809\x190\x1936M\x19=\x191001598\x19-247\x19ATCGAAGATCCATTTGCTGAAGATGACTGGGAAGCT\x197@@@@@C@@@C@C@CC@@@@C@C@C@778771111-\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:36\x19XA:Z:chrVIII,-452209,36M,0;\x19Yt:Z:MM\tHWUSI-EAS1533_0033_FC:1:1:2292:14294\x19161\x19chrVII\x191001598\x190\x1936M\x19=\x191001809\x19247\x19NGCTTTGGACTTGATTGTTGACGCTATCAAGGCTGC\x19)333377777@C@@@C@CCC@@@@C@C@@CC@@@@@\x19NM:i:1\x19MD:Z:0A35\x19AS:i:35\x19XS:i:35\x19XA:Z:chrVIII,+451998,36M,1;\x19Yt:Z:MM\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/pairs_output.stats --- a/test-data/pairs_output.stats Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/pairs_output.stats Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -29,6 +29,33 @@\n summary/frac_cis_40kb+\t0.1383219954648526\n summary/frac_dups\t0.0\n summary/complexity_naive\tnan\n+summary/dist_freq_convergence/convergence_dist\t421697\n+summary/dist_freq_convergence/strands_w_max_convergence_dist\t++\n+summary/dist_freq_convergence/convergence_rel_diff_threshold\t0.05\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/++\t25\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/--\t26\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/-+\t7\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/+-\t383\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist_all_strands\t441\n+summary/dist_freq_convergence/n_cis_pairs_above_convergence_dist_all_strands\t0\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/++\t0.05668934240362812\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/--\t0.05895691609977324\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/-+\t0.015873015873015872\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/+-\t0.8684807256235828\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_cis_in_cis_above_convergence_dist_all_strands\t0.0\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/++\t0.05668934240362812\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/--\t0.05895691609977324\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/-+\t0.015873015873015872\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/+-\t0.8684807256235828\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_above_convergence_dist_all_strands\t0.0\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/++\t0.05668934240362812\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/--\t0.05895691609977324\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/-+\t0.015873015873015872\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/+-\t0.8684807256235828\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_above_convergence_dist_all_strands\t0.0\n chrom_freq/Test_seq/Test_seq\t441\n dist_freq/0-1/+-\t0\n dist_freq/0-1/-+\t0\n@@ -42,144 +69,280 @@\n dist_freq/2-3/-+\t0\n dist_freq/2-3/--\t0\n dist_freq/2-3/++\t0\n-dist_freq/3-6/+-\t0\n-dist_freq/3-6/-+\t0\n-dist_freq/3-6/--\t0\n-dist_freq/3-6/++\t0\n-dist_freq/6-10/+-\t0\n-dist_freq/6-10/-+\t0\n-dist_freq/6-10/--\t0\n-dist_freq/6-10/++\t0\n-dist_freq/10-18/+-\t0\n-dist_freq/10-18/-+\t0\n-dist_freq/10-18/--\t0\n-dist_freq/10-18/++\t0\n-dist_freq/18-32/+-\t0\n-dist_freq/18-32/-+\t0\n-dist_freq/18-32/--\t0\n-dist_freq/18-32/++\t0\n-dist_freq/32-56/+-\t7\n-dist_freq/32-56/-+\t0\n-dist_freq/32-56/--\t0\n-dist_freq/32-56/++\t0\n-dist_freq/56-100/+-\t9\n-dist_freq/56-100/-+\t0\n-dist_freq/56-100/--\t0\n-dist_freq/56-100/++\t0\n-dist_freq/100-178/+-\t5\n-dist_freq/100-178/-+\t0\n-dist_freq/100-178/--\t0\n-dist_freq/100-178/++\t0\n-dist_freq/178-316/+-\t60\n-dist_freq/178-316/-+\t0\n-dist_freq/178-316/--\t0\n-dist_freq/178-316/++\t0\n-dist_freq/316-562/+-\t284\n-dist_freq/316-562/-+\t0\n-dist_freq/316-562/--\t0\n-dist_freq/316-562/++\t0\n-dist_freq/562-1000/+-\t1\n-dist_freq/562-1000/-+\t0\n-dist_freq/562-1000/--\t0\n-dist_freq/562-1000/++\t0\n-dist_freq/1000-1778/+-\t1\n-dist_freq/1000-1778/-+\t0\n-dist_freq/1000-1778/--\t1\n-dist_freq/1000-1778/++\t0\n-dist_freq/1778-3162/+-\t1\n-dist_freq/1778-3162/-+\t0\n-dist_freq/1778-3162/--\t1\n-dist_freq/1778-3162/++\t1\n-dist_freq/3162-5623/+-\t0\n-dist_freq/3162-5623/-+\t0\n-dist_freq/3162-5623/--\t0\n-dist_freq/3162-5623/++\t0\n-dist_freq/5623-10000/+-\t2\n-dist_freq/5623-10000/-+\t0\n-dist_freq/5623-10000/--\t0\n-dist_freq/5623-10000/++\t1\n-dist_freq/10000-177'..b'228/+-\t1\n+dist_freq/237137-316228/-+\t0\n+dist_freq/237137-316228/--\t0\n+dist_freq/237137-316228/++\t0\n+dist_freq/316228-421697/+-\t0\n+dist_freq/316228-421697/-+\t1\n+dist_freq/316228-421697/--\t0\n+dist_freq/316228-421697/++\t0\n+dist_freq/421697-562341/+-\t0\n+dist_freq/421697-562341/-+\t0\n+dist_freq/421697-562341/--\t0\n+dist_freq/421697-562341/++\t0\n+dist_freq/562341-749894/+-\t0\n+dist_freq/562341-749894/-+\t0\n+dist_freq/562341-749894/--\t0\n+dist_freq/562341-749894/++\t0\n+dist_freq/749894-1000000/+-\t0\n+dist_freq/749894-1000000/-+\t0\n+dist_freq/749894-1000000/--\t0\n+dist_freq/749894-1000000/++\t0\n+dist_freq/1000000-1333521/+-\t0\n+dist_freq/1000000-1333521/-+\t0\n+dist_freq/1000000-1333521/--\t0\n+dist_freq/1000000-1333521/++\t0\n+dist_freq/1333521-1778279/+-\t0\n+dist_freq/1333521-1778279/-+\t0\n+dist_freq/1333521-1778279/--\t0\n+dist_freq/1333521-1778279/++\t0\n+dist_freq/1778279-2371374/+-\t0\n+dist_freq/1778279-2371374/-+\t0\n+dist_freq/1778279-2371374/--\t0\n+dist_freq/1778279-2371374/++\t0\n+dist_freq/2371374-3162278/+-\t0\n+dist_freq/2371374-3162278/-+\t0\n+dist_freq/2371374-3162278/--\t0\n+dist_freq/2371374-3162278/++\t0\n+dist_freq/3162278-4216965/+-\t0\n+dist_freq/3162278-4216965/-+\t0\n+dist_freq/3162278-4216965/--\t0\n+dist_freq/3162278-4216965/++\t0\n+dist_freq/4216965-5623413/+-\t0\n+dist_freq/4216965-5623413/-+\t0\n+dist_freq/4216965-5623413/--\t0\n+dist_freq/4216965-5623413/++\t0\n+dist_freq/5623413-7498942/+-\t0\n+dist_freq/5623413-7498942/-+\t0\n+dist_freq/5623413-7498942/--\t0\n+dist_freq/5623413-7498942/++\t0\n+dist_freq/7498942-10000000/+-\t0\n+dist_freq/7498942-10000000/-+\t0\n+dist_freq/7498942-10000000/--\t0\n+dist_freq/7498942-10000000/++\t0\n+dist_freq/10000000-13335214/+-\t0\n+dist_freq/10000000-13335214/-+\t0\n+dist_freq/10000000-13335214/--\t0\n+dist_freq/10000000-13335214/++\t0\n+dist_freq/13335214-17782794/+-\t0\n+dist_freq/13335214-17782794/-+\t0\n+dist_freq/13335214-17782794/--\t0\n+dist_freq/13335214-17782794/++\t0\n+dist_freq/17782794-23713737/+-\t0\n+dist_freq/17782794-23713737/-+\t0\n+dist_freq/17782794-23713737/--\t0\n+dist_freq/17782794-23713737/++\t0\n+dist_freq/23713737-31622777/+-\t0\n+dist_freq/23713737-31622777/-+\t0\n+dist_freq/23713737-31622777/--\t0\n+dist_freq/23713737-31622777/++\t0\n+dist_freq/31622777-42169650/+-\t0\n+dist_freq/31622777-42169650/-+\t0\n+dist_freq/31622777-42169650/--\t0\n+dist_freq/31622777-42169650/++\t0\n+dist_freq/42169650-56234133/+-\t0\n+dist_freq/42169650-56234133/-+\t0\n+dist_freq/42169650-56234133/--\t0\n+dist_freq/42169650-56234133/++\t0\n+dist_freq/56234133-74989421/+-\t0\n+dist_freq/56234133-74989421/-+\t0\n+dist_freq/56234133-74989421/--\t0\n+dist_freq/56234133-74989421/++\t0\n+dist_freq/74989421-100000000/+-\t0\n+dist_freq/74989421-100000000/-+\t0\n+dist_freq/74989421-100000000/--\t0\n+dist_freq/74989421-100000000/++\t0\n+dist_freq/100000000-133352143/+-\t0\n+dist_freq/100000000-133352143/-+\t0\n+dist_freq/100000000-133352143/--\t0\n+dist_freq/100000000-133352143/++\t0\n+dist_freq/133352143-177827941/+-\t0\n+dist_freq/133352143-177827941/-+\t0\n+dist_freq/133352143-177827941/--\t0\n+dist_freq/133352143-177827941/++\t0\n+dist_freq/177827941-237137371/+-\t0\n+dist_freq/177827941-237137371/-+\t0\n+dist_freq/177827941-237137371/--\t0\n+dist_freq/177827941-237137371/++\t0\n+dist_freq/237137371-316227766/+-\t0\n+dist_freq/237137371-316227766/-+\t0\n+dist_freq/237137371-316227766/--\t0\n+dist_freq/237137371-316227766/++\t0\n+dist_freq/316227766-421696503/+-\t0\n+dist_freq/316227766-421696503/-+\t0\n+dist_freq/316227766-421696503/--\t0\n+dist_freq/316227766-421696503/++\t0\n+dist_freq/421696503-562341325/+-\t0\n+dist_freq/421696503-562341325/-+\t0\n+dist_freq/421696503-562341325/--\t0\n+dist_freq/421696503-562341325/++\t0\n+dist_freq/562341325-749894209/+-\t0\n+dist_freq/562341325-749894209/-+\t0\n+dist_freq/562341325-749894209/--\t0\n+dist_freq/562341325-749894209/++\t0\n+dist_freq/749894209-1000000000/+-\t0\n+dist_freq/749894209-1000000000/-+\t0\n+dist_freq/749894209-1000000000/--\t0\n+dist_freq/749894209-1000000000/++\t0\n+dist_freq/1000000000+/+-\t0\n+dist_freq/1000000000+/-+\t0\n+dist_freq/1000000000+/--\t0\n+dist_freq/1000000000+/++\t0\n chromsizes/Test_seq\t450060\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/pairs_output_merged.stats --- a/test-data/pairs_output_merged.stats Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/pairs_output_merged.stats Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -7,28 +7,55 @@\n cis\t882\n trans\t0\n pair_types/NU\t2\n-pair_types/UR\t38\n+pair_types/RU\t34\n pair_types/MR\t12\n-pair_types/MU\t42\n pair_types/UU\t810\n-pair_types/RU\t34\n pair_types/NR\t238\n+pair_types/MU\t42\n pair_types/MM\t8\n+pair_types/UR\t38\n cis_1kb+\t150\n cis_2kb+\t144\n cis_4kb+\t140\n cis_10kb+\t134\n cis_20kb+\t122\n cis_40kb+\t122\n+summary/frac_cis\t1.0\n summary/frac_cis_1kb+\t0.17006802721088435\n-summary/frac_dups\t0.0\n-summary/frac_cis_10kb+\t0.15192743764172337\n-summary/complexity_naive\tnan\n-summary/frac_cis\t1.0\n summary/frac_cis_2kb+\t0.16326530612244897\n summary/frac_cis_4kb+\t0.15873015873015872\n+summary/frac_cis_10kb+\t0.15192743764172337\n summary/frac_cis_20kb+\t0.1383219954648526\n summary/frac_cis_40kb+\t0.1383219954648526\n+summary/frac_dups\t0.0\n+summary/complexity_naive\tnan\n+summary/dist_freq_convergence/convergence_dist\t421697\n+summary/dist_freq_convergence/strands_w_max_convergence_dist\t++\n+summary/dist_freq_convergence/convergence_rel_diff_threshold\t0.05\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/++\t50\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/--\t52\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/-+\t14\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/+-\t766\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist_all_strands\t882\n+summary/dist_freq_convergence/n_cis_pairs_above_convergence_dist_all_strands\t0\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/++\t0.05668934240362812\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/--\t0.05895691609977324\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/-+\t0.015873015873015872\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/+-\t0.8684807256235828\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_cis_in_cis_above_convergence_dist_all_strands\t0.0\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/++\t0.05668934240362812\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/--\t0.05895691609977324\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/-+\t0.015873015873015872\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/+-\t0.8684807256235828\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_above_convergence_dist_all_strands\t0.0\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/++\t0.05668934240362812\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/--\t0.05895691609977324\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/-+\t0.015873015873015872\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/+-\t0.8684807256235828\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_above_convergence_dist_all_strands\t0.0\n chrom_freq/Test_seq/Test_seq\t882\n dist_freq/0-1/+-\t0\n dist_freq/0-1/-+\t0\n@@ -42,144 +69,280 @@\n dist_freq/2-3/-+\t0\n dist_freq/2-3/--\t0\n dist_freq/2-3/++\t0\n-dist_freq/3-6/+-\t0\n-dist_freq/3-6/-+\t0\n-dist_freq/3-6/--\t0\n-dist_freq/3-6/++\t0\n-dist_freq/6-10/+-\t0\n-dist_freq/6-10/-+\t0\n-dist_freq/6-10/--\t0\n-dist_freq/6-10/++\t0\n-dist_freq/10-18/+-\t120\n-dist_freq/10-18/-+\t0\n-dist_freq/10-18/--\t0\n-dist_freq/10-18/++\t0\n-dist_freq/18-32/+-\t2\n-dist_freq/18-32/-+\t0\n-dist_freq/18-32/--\t0\n-dist_freq/18-32/++\t0\n-dist_freq/32-56/+-\t0\n-dist_freq/32-56/-+\t0\n-dist_freq/32-56/--\t0\n-dist_freq/32-56/++\t0\n-dist_freq/56-100/+-\t0\n-dist_freq/56-100/-+\t0\n-dist_freq/56-100/--\t0\n-dist_freq/56-100/++\t0\n-dist_freq/100-178/+-\t0\n-dist_freq/100-178/-+\t0\n-dist_freq/100-178/--\t0\n-dist_freq/100-178/++\t0\n-dist_freq/178-316/+-\t0\n-dist_freq/178-316/-+\t0\n-dist_freq/178-316/--\t0\n-'..b'228/+-\t1\n+dist_freq/237137-316228/-+\t0\n+dist_freq/237137-316228/--\t0\n+dist_freq/237137-316228/++\t0\n+dist_freq/316228-421697/+-\t0\n+dist_freq/316228-421697/-+\t2\n+dist_freq/316228-421697/--\t0\n+dist_freq/316228-421697/++\t0\n+dist_freq/421697-562341/+-\t0\n+dist_freq/421697-562341/-+\t0\n+dist_freq/421697-562341/--\t0\n+dist_freq/421697-562341/++\t0\n+dist_freq/562341-749894/+-\t0\n+dist_freq/562341-749894/-+\t0\n+dist_freq/562341-749894/--\t0\n+dist_freq/562341-749894/++\t0\n+dist_freq/749894-1000000/+-\t0\n+dist_freq/749894-1000000/-+\t0\n+dist_freq/749894-1000000/--\t0\n+dist_freq/749894-1000000/++\t0\n+dist_freq/1000000-1333521/+-\t0\n+dist_freq/1000000-1333521/-+\t0\n+dist_freq/1000000-1333521/--\t0\n+dist_freq/1000000-1333521/++\t0\n+dist_freq/1333521-1778279/+-\t0\n+dist_freq/1333521-1778279/-+\t0\n+dist_freq/1333521-1778279/--\t0\n+dist_freq/1333521-1778279/++\t0\n+dist_freq/1778279-2371374/+-\t0\n+dist_freq/1778279-2371374/-+\t0\n+dist_freq/1778279-2371374/--\t0\n+dist_freq/1778279-2371374/++\t0\n+dist_freq/2371374-3162278/+-\t0\n+dist_freq/2371374-3162278/-+\t0\n+dist_freq/2371374-3162278/--\t0\n+dist_freq/2371374-3162278/++\t0\n+dist_freq/3162278-4216965/+-\t0\n+dist_freq/3162278-4216965/-+\t0\n+dist_freq/3162278-4216965/--\t0\n+dist_freq/3162278-4216965/++\t0\n+dist_freq/4216965-5623413/+-\t0\n+dist_freq/4216965-5623413/-+\t0\n+dist_freq/4216965-5623413/--\t0\n+dist_freq/4216965-5623413/++\t0\n+dist_freq/5623413-7498942/+-\t0\n+dist_freq/5623413-7498942/-+\t0\n+dist_freq/5623413-7498942/--\t0\n+dist_freq/5623413-7498942/++\t0\n+dist_freq/7498942-10000000/+-\t0\n+dist_freq/7498942-10000000/-+\t0\n+dist_freq/7498942-10000000/--\t0\n+dist_freq/7498942-10000000/++\t0\n+dist_freq/10000000-13335214/+-\t0\n+dist_freq/10000000-13335214/-+\t0\n+dist_freq/10000000-13335214/--\t0\n+dist_freq/10000000-13335214/++\t0\n+dist_freq/13335214-17782794/+-\t0\n+dist_freq/13335214-17782794/-+\t0\n+dist_freq/13335214-17782794/--\t0\n+dist_freq/13335214-17782794/++\t0\n+dist_freq/17782794-23713737/+-\t0\n+dist_freq/17782794-23713737/-+\t0\n+dist_freq/17782794-23713737/--\t0\n+dist_freq/17782794-23713737/++\t0\n+dist_freq/23713737-31622777/+-\t0\n+dist_freq/23713737-31622777/-+\t0\n+dist_freq/23713737-31622777/--\t0\n+dist_freq/23713737-31622777/++\t0\n+dist_freq/31622777-42169650/+-\t0\n+dist_freq/31622777-42169650/-+\t0\n+dist_freq/31622777-42169650/--\t0\n+dist_freq/31622777-42169650/++\t0\n+dist_freq/42169650-56234133/+-\t0\n+dist_freq/42169650-56234133/-+\t0\n+dist_freq/42169650-56234133/--\t0\n+dist_freq/42169650-56234133/++\t0\n+dist_freq/56234133-74989421/+-\t0\n+dist_freq/56234133-74989421/-+\t0\n+dist_freq/56234133-74989421/--\t0\n+dist_freq/56234133-74989421/++\t0\n+dist_freq/74989421-100000000/+-\t0\n+dist_freq/74989421-100000000/-+\t0\n+dist_freq/74989421-100000000/--\t0\n+dist_freq/74989421-100000000/++\t0\n+dist_freq/100000000-133352143/+-\t0\n+dist_freq/100000000-133352143/-+\t0\n+dist_freq/100000000-133352143/--\t0\n+dist_freq/100000000-133352143/++\t0\n+dist_freq/133352143-177827941/+-\t0\n+dist_freq/133352143-177827941/-+\t0\n+dist_freq/133352143-177827941/--\t0\n+dist_freq/133352143-177827941/++\t0\n+dist_freq/177827941-237137371/+-\t0\n+dist_freq/177827941-237137371/-+\t0\n+dist_freq/177827941-237137371/--\t0\n+dist_freq/177827941-237137371/++\t0\n+dist_freq/237137371-316227766/+-\t0\n+dist_freq/237137371-316227766/-+\t0\n+dist_freq/237137371-316227766/--\t0\n+dist_freq/237137371-316227766/++\t0\n+dist_freq/316227766-421696503/+-\t0\n+dist_freq/316227766-421696503/-+\t0\n+dist_freq/316227766-421696503/--\t0\n+dist_freq/316227766-421696503/++\t0\n+dist_freq/421696503-562341325/+-\t0\n+dist_freq/421696503-562341325/-+\t0\n+dist_freq/421696503-562341325/--\t0\n+dist_freq/421696503-562341325/++\t0\n+dist_freq/562341325-749894209/+-\t0\n+dist_freq/562341325-749894209/-+\t0\n+dist_freq/562341325-749894209/--\t0\n+dist_freq/562341325-749894209/++\t0\n+dist_freq/749894209-1000000000/+-\t0\n+dist_freq/749894209-1000000000/-+\t0\n+dist_freq/749894209-1000000000/--\t0\n+dist_freq/749894209-1000000000/++\t0\n+dist_freq/1000000000+/+-\t0\n+dist_freq/1000000000+/-+\t0\n+dist_freq/1000000000+/--\t0\n+dist_freq/1000000000+/++\t0\n chromsizes/Test_seq\t450060\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/pairs_output_with_chromsize.stats --- a/test-data/pairs_output_with_chromsize.stats Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/pairs_output_with_chromsize.stats Tue Apr 30 12:02:29 2024 +0000 |
| b |
| b'@@ -29,6 +29,33 @@\n summary/frac_cis_40kb+\t0.1383219954648526\n summary/frac_dups\t0.0\n summary/complexity_naive\tnan\n+summary/dist_freq_convergence/convergence_dist\t421697\n+summary/dist_freq_convergence/strands_w_max_convergence_dist\t++\n+summary/dist_freq_convergence/convergence_rel_diff_threshold\t0.05\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/++\t25\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/--\t26\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/-+\t7\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/+-\t383\n+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist_all_strands\t441\n+summary/dist_freq_convergence/n_cis_pairs_above_convergence_dist_all_strands\t0\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/++\t0.05668934240362812\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/--\t0.05895691609977324\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/-+\t0.015873015873015872\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/+-\t0.8684807256235828\n+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_cis_in_cis_above_convergence_dist_all_strands\t0.0\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/++\t0.05668934240362812\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/--\t0.05895691609977324\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/-+\t0.015873015873015872\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/+-\t0.8684807256235828\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_total_mapped_in_cis_above_convergence_dist_all_strands\t0.0\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/++\t0.05668934240362812\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/--\t0.05895691609977324\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/-+\t0.015873015873015872\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/+-\t0.8684807256235828\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist_all_strands\t1.0\n+summary/dist_freq_convergence/frac_total_nodups_in_cis_above_convergence_dist_all_strands\t0.0\n chrom_freq/Test_seq/Test_seq\t441\n dist_freq/0-1/+-\t0\n dist_freq/0-1/-+\t0\n@@ -42,144 +69,280 @@\n dist_freq/2-3/-+\t0\n dist_freq/2-3/--\t0\n dist_freq/2-3/++\t0\n-dist_freq/3-6/+-\t0\n-dist_freq/3-6/-+\t0\n-dist_freq/3-6/--\t0\n-dist_freq/3-6/++\t0\n-dist_freq/6-10/+-\t0\n-dist_freq/6-10/-+\t0\n-dist_freq/6-10/--\t0\n-dist_freq/6-10/++\t0\n-dist_freq/10-18/+-\t0\n-dist_freq/10-18/-+\t0\n-dist_freq/10-18/--\t0\n-dist_freq/10-18/++\t0\n-dist_freq/18-32/+-\t0\n-dist_freq/18-32/-+\t0\n-dist_freq/18-32/--\t0\n-dist_freq/18-32/++\t0\n-dist_freq/32-56/+-\t7\n-dist_freq/32-56/-+\t0\n-dist_freq/32-56/--\t0\n-dist_freq/32-56/++\t0\n-dist_freq/56-100/+-\t9\n-dist_freq/56-100/-+\t0\n-dist_freq/56-100/--\t0\n-dist_freq/56-100/++\t0\n-dist_freq/100-178/+-\t5\n-dist_freq/100-178/-+\t0\n-dist_freq/100-178/--\t0\n-dist_freq/100-178/++\t0\n-dist_freq/178-316/+-\t60\n-dist_freq/178-316/-+\t0\n-dist_freq/178-316/--\t0\n-dist_freq/178-316/++\t0\n-dist_freq/316-562/+-\t284\n-dist_freq/316-562/-+\t0\n-dist_freq/316-562/--\t0\n-dist_freq/316-562/++\t0\n-dist_freq/562-1000/+-\t1\n-dist_freq/562-1000/-+\t0\n-dist_freq/562-1000/--\t0\n-dist_freq/562-1000/++\t0\n-dist_freq/1000-1778/+-\t1\n-dist_freq/1000-1778/-+\t0\n-dist_freq/1000-1778/--\t1\n-dist_freq/1000-1778/++\t0\n-dist_freq/1778-3162/+-\t1\n-dist_freq/1778-3162/-+\t0\n-dist_freq/1778-3162/--\t1\n-dist_freq/1778-3162/++\t1\n-dist_freq/3162-5623/+-\t0\n-dist_freq/3162-5623/-+\t0\n-dist_freq/3162-5623/--\t0\n-dist_freq/3162-5623/++\t0\n-dist_freq/5623-10000/+-\t2\n-dist_freq/5623-10000/-+\t0\n-dist_freq/5623-10000/--\t0\n-dist_freq/5623-10000/++\t1\n-dist_freq/10000-177'..b'228/+-\t1\n+dist_freq/237137-316228/-+\t0\n+dist_freq/237137-316228/--\t0\n+dist_freq/237137-316228/++\t0\n+dist_freq/316228-421697/+-\t0\n+dist_freq/316228-421697/-+\t1\n+dist_freq/316228-421697/--\t0\n+dist_freq/316228-421697/++\t0\n+dist_freq/421697-562341/+-\t0\n+dist_freq/421697-562341/-+\t0\n+dist_freq/421697-562341/--\t0\n+dist_freq/421697-562341/++\t0\n+dist_freq/562341-749894/+-\t0\n+dist_freq/562341-749894/-+\t0\n+dist_freq/562341-749894/--\t0\n+dist_freq/562341-749894/++\t0\n+dist_freq/749894-1000000/+-\t0\n+dist_freq/749894-1000000/-+\t0\n+dist_freq/749894-1000000/--\t0\n+dist_freq/749894-1000000/++\t0\n+dist_freq/1000000-1333521/+-\t0\n+dist_freq/1000000-1333521/-+\t0\n+dist_freq/1000000-1333521/--\t0\n+dist_freq/1000000-1333521/++\t0\n+dist_freq/1333521-1778279/+-\t0\n+dist_freq/1333521-1778279/-+\t0\n+dist_freq/1333521-1778279/--\t0\n+dist_freq/1333521-1778279/++\t0\n+dist_freq/1778279-2371374/+-\t0\n+dist_freq/1778279-2371374/-+\t0\n+dist_freq/1778279-2371374/--\t0\n+dist_freq/1778279-2371374/++\t0\n+dist_freq/2371374-3162278/+-\t0\n+dist_freq/2371374-3162278/-+\t0\n+dist_freq/2371374-3162278/--\t0\n+dist_freq/2371374-3162278/++\t0\n+dist_freq/3162278-4216965/+-\t0\n+dist_freq/3162278-4216965/-+\t0\n+dist_freq/3162278-4216965/--\t0\n+dist_freq/3162278-4216965/++\t0\n+dist_freq/4216965-5623413/+-\t0\n+dist_freq/4216965-5623413/-+\t0\n+dist_freq/4216965-5623413/--\t0\n+dist_freq/4216965-5623413/++\t0\n+dist_freq/5623413-7498942/+-\t0\n+dist_freq/5623413-7498942/-+\t0\n+dist_freq/5623413-7498942/--\t0\n+dist_freq/5623413-7498942/++\t0\n+dist_freq/7498942-10000000/+-\t0\n+dist_freq/7498942-10000000/-+\t0\n+dist_freq/7498942-10000000/--\t0\n+dist_freq/7498942-10000000/++\t0\n+dist_freq/10000000-13335214/+-\t0\n+dist_freq/10000000-13335214/-+\t0\n+dist_freq/10000000-13335214/--\t0\n+dist_freq/10000000-13335214/++\t0\n+dist_freq/13335214-17782794/+-\t0\n+dist_freq/13335214-17782794/-+\t0\n+dist_freq/13335214-17782794/--\t0\n+dist_freq/13335214-17782794/++\t0\n+dist_freq/17782794-23713737/+-\t0\n+dist_freq/17782794-23713737/-+\t0\n+dist_freq/17782794-23713737/--\t0\n+dist_freq/17782794-23713737/++\t0\n+dist_freq/23713737-31622777/+-\t0\n+dist_freq/23713737-31622777/-+\t0\n+dist_freq/23713737-31622777/--\t0\n+dist_freq/23713737-31622777/++\t0\n+dist_freq/31622777-42169650/+-\t0\n+dist_freq/31622777-42169650/-+\t0\n+dist_freq/31622777-42169650/--\t0\n+dist_freq/31622777-42169650/++\t0\n+dist_freq/42169650-56234133/+-\t0\n+dist_freq/42169650-56234133/-+\t0\n+dist_freq/42169650-56234133/--\t0\n+dist_freq/42169650-56234133/++\t0\n+dist_freq/56234133-74989421/+-\t0\n+dist_freq/56234133-74989421/-+\t0\n+dist_freq/56234133-74989421/--\t0\n+dist_freq/56234133-74989421/++\t0\n+dist_freq/74989421-100000000/+-\t0\n+dist_freq/74989421-100000000/-+\t0\n+dist_freq/74989421-100000000/--\t0\n+dist_freq/74989421-100000000/++\t0\n+dist_freq/100000000-133352143/+-\t0\n+dist_freq/100000000-133352143/-+\t0\n+dist_freq/100000000-133352143/--\t0\n+dist_freq/100000000-133352143/++\t0\n+dist_freq/133352143-177827941/+-\t0\n+dist_freq/133352143-177827941/-+\t0\n+dist_freq/133352143-177827941/--\t0\n+dist_freq/133352143-177827941/++\t0\n+dist_freq/177827941-237137371/+-\t0\n+dist_freq/177827941-237137371/-+\t0\n+dist_freq/177827941-237137371/--\t0\n+dist_freq/177827941-237137371/++\t0\n+dist_freq/237137371-316227766/+-\t0\n+dist_freq/237137371-316227766/-+\t0\n+dist_freq/237137371-316227766/--\t0\n+dist_freq/237137371-316227766/++\t0\n+dist_freq/316227766-421696503/+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chromsizes/Test_seq\t450060\n' |
| b |
| diff -r 5412142130ad -r 55a53b5e308d test-data/pairs_output_yaml.stats --- a/test-data/pairs_output_yaml.stats Tue Apr 16 12:51:21 2024 +0000 +++ b/test-data/pairs_output_yaml.stats Tue Apr 30 12:02:29 2024 +0000 |
| b |
| @@ -3,10 +3,8 @@ total_unmapped: 4 total_single_sided_mapped: 147 total_mapped: 441 - total_dups: 0 total_nodups: 441 cis: 441 - trans: 0 pair_types: UU: 405 NR: 119 @@ -32,6 +30,38 @@ frac_cis_40kb+: 0.1383219954648526 frac_dups: 0.0 complexity_naive: .nan + dist_freq_convergence: + convergence_dist: 421697 + strands_w_max_convergence_dist: ++ + convergence_rel_diff_threshold: 0.05 + n_cis_pairs_below_convergence_dist: + ++: 25 + --: 26 + -+: 7 + +-: 383 + n_cis_pairs_below_convergence_dist_all_strands: 441 + n_cis_pairs_above_convergence_dist_all_strands: 0 + frac_cis_in_cis_below_convergence_dist: + ++: 0.05668934240362812 + --: 0.05895691609977324 + -+: 0.015873015873015872 + +-: 0.8684807256235828 + frac_cis_in_cis_below_convergence_dist_all_strands: 1.0 + frac_cis_in_cis_above_convergence_dist_all_strands: 0.0 + frac_total_mapped_in_cis_below_convergence_dist: + ++: 0.05668934240362812 + --: 0.05895691609977324 + -+: 0.015873015873015872 + +-: 0.8684807256235828 + frac_total_mapped_in_cis_below_convergence_dist_all_strands: 1.0 + frac_total_mapped_in_cis_above_convergence_dist_all_strands: 0.0 + frac_total_nodups_in_cis_below_convergence_dist: + ++: 0.05668934240362812 + --: 0.05895691609977324 + -+: 0.015873015873015872 + +-: 0.8684807256235828 + frac_total_nodups_in_cis_below_convergence_dist_all_strands: 1.0 + frac_total_nodups_in_cis_above_convergence_dist_all_strands: 0.0 chrom_freq: Test_seq/Test_seq: 441 dist_freq: @@ -40,156 +70,292 @@ 1: 0 2: 0 3: 0 + 4: 0 6: 0 + 7: 0 10: 0 + 13: 0 18: 0 - 32: 7 - 56: 9 - 100: 5 - 178: 60 - 316: 284 - 562: 1 - 1000: 1 - 1778: 1 + 24: 0 + 32: 0 + 42: 7 + 56: 7 + 75: 2 + 100: 3 + 133: 2 + 178: 3 + 237: 57 + 316: 171 + 422: 113 + 562: 0 + 750: 1 + 1000: 0 + 1334: 1 + 1778: 0 + 2371: 1 3162: 0 - 5623: 2 - 10000: 2 + 4217: 0 + 5623: 0 + 7499: 2 + 10000: 1 + 13335: 1 17783: 1 + 23714: 0 31623: 0 - 56234: 3 - 100000: 3 - 177828: 4 + 42170: 0 + 56234: 2 + 74989: 1 + 100000: 1 + 133352: 2 + 177828: 3 + 237137: 1 316228: 0 + 421697: 0 562341: 0 + 749894: 0 1000000: 0 + 1333521: 0 1778279: 0 + 2371374: 0 3162278: 0 + 4216965: 0 5623413: 0 + 7498942: 0 10000000: 0 + 13335214: 0 17782794: 0 + 23713737: 0 31622777: 0 + 42169650: 0 56234133: 0 + 74989421: 0 100000000: 0 + 133352143: 0 177827941: 0 + 237137371: 0 316227766: 0 + 421696503: 0 562341325: 0 + 749894209: 0 1000000000: 0 -+: 0: 0 1: 0 2: 0 3: 0 + 4: 0 6: 0 + 7: 0 10: 0 + 13: 0 18: 0 + 24: 0 32: 0 + 42: 0 56: 0 + 75: 0 100: 0 + 133: 0 178: 0 + 237: 0 316: 0 + 422: 0 562: 0 + 750: 0 1000: 0 + 1334: 0 1778: 0 + 2371: 0 3162: 0 + 4217: 0 5623: 0 - 10000: 2 + 7499: 0 + 10000: 1 + 13335: 1 17783: 0 - 31623: 1 + 23714: 0 + 31623: 0 + 42170: 1 56234: 0 - 100000: 3 + 74989: 0 + 100000: 0 + 133352: 3 177828: 0 + 237137: 0 316228: 1 + 421697: 0 562341: 0 + 749894: 0 1000000: 0 + 1333521: 0 1778279: 0 + 2371374: 0 3162278: 0 + 4216965: 0 5623413: 0 + 7498942: 0 10000000: 0 + 13335214: 0 17782794: 0 + 23713737: 0 31622777: 0 + 42169650: 0 56234133: 0 + 74989421: 0 100000000: 0 + 133352143: 0 177827941: 0 + 237137371: 0 316227766: 0 + 421696503: 0 562341325: 0 + 749894209: 0 1000000000: 0 --: 0: 0 1: 0 2: 0 3: 0 + 4: 0 6: 0 + 7: 0 10: 0 + 13: 0 18: 0 + 24: 0 32: 0 + 42: 0 56: 0 + 75: 0 100: 0 + 133: 0 178: 0 + 237: 0 316: 0 + 422: 0 562: 0 + 750: 0 1000: 1 - 1778: 1 + 1334: 0 + 1778: 0 + 2371: 1 3162: 0 + 4217: 0 5623: 0 + 7499: 0 10000: 0 + 13335: 0 17783: 0 - 31623: 21 + 23714: 0 + 31623: 0 + 42170: 21 56234: 1 + 74989: 0 100000: 2 + 133352: 0 177828: 0 + 237137: 0 316228: 0 + 421697: 0 562341: 0 + 749894: 0 1000000: 0 + 1333521: 0 1778279: 0 + 2371374: 0 3162278: 0 + 4216965: 0 5623413: 0 + 7498942: 0 10000000: 0 + 13335214: 0 17782794: 0 + 23713737: 0 31622777: 0 + 42169650: 0 56234133: 0 + 74989421: 0 100000000: 0 + 133352143: 0 177827941: 0 + 237137371: 0 316227766: 0 + 421696503: 0 562341325: 0 + 749894209: 0 1000000000: 0 ++: 0: 0 1: 0 2: 0 3: 0 + 4: 0 6: 0 + 7: 0 10: 0 + 13: 0 18: 0 + 24: 0 32: 0 + 42: 0 56: 0 + 75: 0 100: 0 + 133: 0 178: 0 + 237: 0 316: 0 + 422: 0 562: 0 + 750: 0 1000: 0 + 1334: 0 1778: 1 + 2371: 0 3162: 0 + 4217: 0 5623: 1 + 7499: 0 10000: 1 + 13335: 0 17783: 0 - 31623: 10 - 56234: 3 - 100000: 7 + 23714: 0 + 31623: 0 + 42170: 10 + 56234: 2 + 74989: 1 + 100000: 4 + 133352: 3 177828: 2 + 237137: 0 316228: 0 + 421697: 0 562341: 0 + 749894: 0 1000000: 0 + 1333521: 0 1778279: 0 + 2371374: 0 3162278: 0 + 4216965: 0 5623413: 0 + 7498942: 0 10000000: 0 + 13335214: 0 17782794: 0 + 23713737: 0 31622777: 0 + 42169650: 0 56234133: 0 + 74989421: 0 100000000: 0 + 133352143: 0 177827941: 0 + 237137371: 0 316227766: 0 + 421696503: 0 562341325: 0 + 749894209: 0 1000000000: 0 chromsizes: Test_seq: 450060 |