Mercurial > repos > iuc > pairtools_split
comparison test-data/output_parsed_pairs_bam_5unique.pairs @ 3:060f0fed864e draft
planemo upload for repository https://github.com/open2c/pairtools commit 162c595b19e442f40be4c2f5434b20b56ade52d4
author | iuc |
---|---|
date | Tue, 30 Apr 2024 12:02:15 +0000 |
parents | bffcba7ce9b5 |
children | 39df08e91cdf |
comparison
equal
deleted
inserted
replaced
2:53d73d58e105 | 3:060f0fed864e |
---|---|
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/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 | 40 #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 |
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/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 | 42 #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 |
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/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 | 44 #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 |
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/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 | 47 #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 |
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 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 | 49 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 |
50 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 | 50 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 |
51 HWUSI-EAS1533_0033_FC:1:1:1160:9629 ! 0 ! 0 - - XX HWUSI-EAS1533_0033_FC:1:1:1160:9629129chrI108076036MchrX4486200NCCATGGTCTAAGAGTTTCTCCAAACGCCTAATGTA&,,,,1111/:::::@@@@@@@@@@@@@@@@@@@@<NM:i:1MD:Z:0C35AS:i:35XS:i:0Yt:Z:XX | 51 HWUSI-EAS1533_0033_FC:1:1:1160:9629 ! 0 ! 0 - - XX HWUSI-EAS1533_0033_FC:1:1:1160:9629129chrI108076036MchrX4486200NCCATGGTCTAAGAGTTTCTCCAAACGCCTAATGTA&,,,,1111/:::::@@@@@@@@@@@@@@@@@@@@<NM:i:1MD:Z:0C35AS:i:35XS:i:0Yt:Z:XX |
52 HWUSI-EAS1533_0033_FC:1:1:1179:5315 ! 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 HWUSI-EAS1533_0033_FC:1:1:1179:5315 ! 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 |