Mercurial > repos > iuc > pairtools_parse

comparison test-data/output_parsed_pairs_bam_readid_dropped.pairs @ 8:44cb74c154bc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/open2c/pairtools commit 162c595b19e442f40be4c2f5434b20b56ade52d4
author iuc
date Tue, 30 Apr 2024 12:03:00 +0000
parents 68413c5eb035
children d3a7b17714c1
comparison
equal deleted inserted replaced
7:b0a1f128fa15 8:44cb74c154bc
35 #samheader: @SQ SN:chrXIII LN:924431 35 #samheader: @SQ SN:chrXIII LN:924431
36 #samheader: @SQ SN:chrXIV LN:784333 36 #samheader: @SQ SN:chrXIV LN:784333
37 #samheader: @SQ SN:chrXV LN:1091291 37 #samheader: @SQ SN:chrXV LN:1091291
38 #samheader: @SQ SN:chrXVI LN:948066 38 #samheader: @SQ SN:chrXVI LN:948066
39 #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 39 #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
40 #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 40 #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
41 #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 41 #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
42 #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 42 #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
43 #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 43 #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
44 #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 44 #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
45 #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 45 #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
46 #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 46 #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
47 #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 47 #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
48 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 48 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2
49 . ! 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 49 . ! 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
50 . 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 50 . 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
51 . ! 0 ! 0 - - XX HWUSI-EAS1533_0033_FC:1:1:1160:9629129chrI108076036MchrX4486200NCCATGGTCTAAGAGTTTCTCCAAACGCCTAATGTA&,,,,1111/:::::@@@@@@@@@@@@@@@@@@@@<NM:i:1MD:Z:0C35AS:i:35XS:i:0Yt:Z:XX 51 . ! 0 ! 0 - - XX HWUSI-EAS1533_0033_FC:1:1:1160:9629129chrI108076036MchrX4486200NCCATGGTCTAAGAGTTTCTCCAAACGCCTAATGTA&,,,,1111/:::::@@@@@@@@@@@@@@@@@@@@<NM:i:1MD:Z:0C35AS:i:35XS:i:0Yt:Z:XX
52 . ! 0 chrI 11122 - + NU HWUSI-EAS1533_0033_FC:1:1:1179:5315133chrI111220*=111220NGTGTGGTGTGTGGGGGTGGTGTGGGTGTGGGGGGG####################################AS:i:0XS:i:0Yt:Z:NU HWUSI-EAS1533_0033_FC:1:1:1179:531573chrI111226036M=111220GTTATTAATTGGATAAATAGTATTTTTCTTGGCATT-332022222838882122258888222222::::@NM:i:1MD:Z:0T35AS:i:35XS:i:0Yt:Z:NU 52 . ! 0 chrI 11122 - + NU HWUSI-EAS1533_0033_FC:1:1:1179:5315133chrI111220*=111220NGTGTGGTGTGTGGGGGTGGTGTGGGTGTGGGGGGG####################################AS:i:0XS:i:0Yt:Z:NU HWUSI-EAS1533_0033_FC:1:1:1179:531573chrI111226036M=111220GTTATTAATTGGATAAATAGTATTTTTCTTGGCATT-332022222838882122258888222222::::@NM:i:1MD:Z:0T35AS:i:35XS:i:0Yt:Z:NU