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comparison test-data/output_sorted_pairs.pairs @ 5:8ed44487c834 draft

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planemo upload for repository https://github.com/open2c/pairtools commit 162c595b19e442f40be4c2f5434b20b56ade52d4
author iuc
date Tue, 30 Apr 2024 12:02:44 +0000
parents 9179bf8f4ae1
children fdd073110081
comparison
equal deleted inserted replaced
4:8cffb8fc34f0 5:8ed44487c834
36 #samheader: @SQ SN:chrXIII LN:924431 36 #samheader: @SQ SN:chrXIII LN:924431
37 #samheader: @SQ SN:chrXIV LN:784333 37 #samheader: @SQ SN:chrXIV LN:784333
38 #samheader: @SQ SN:chrXV LN:1091291 38 #samheader: @SQ SN:chrXV LN:1091291
39 #samheader: @SQ SN:chrXVI LN:948066 39 #samheader: @SQ SN:chrXVI LN:948066
40 #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: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
41 #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 41 #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
42 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/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 PP:pairtools_parse-1.2 VN:1.0.3 42 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/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 PP:pairtools_parse-1.2 VN:1.1.0
43 #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 43 #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
44 #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 44 #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
45 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/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 PP:pairtools_parse-2.2 VN:1.0.3 45 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/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 PP:pairtools_parse-2.2 VN:1.1.0
46 #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 46 #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
47 #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 47 #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
48 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/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 PP:pairtools_parse-3.2 VN:1.0.3 48 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/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 PP:pairtools_parse-3.2 VN:1.1.0
49 #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 49 #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
50 #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 50 #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
51 #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 51 #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
52 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/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 PP:pairtools_parse-4.3 VN:1.0.3 52 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/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 PP:pairtools_parse-4.3 VN:1.1.0
53 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 53 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2
54 HWUSI-EAS1533_0033_FC:1:1:1193:16038 ! 0 ! 0 - - MM HWUSI-EAS1533_0033_FC:1:1:1193:1603881chrIV1529635036MchrIX187220AATTGACATTAAGCAATTGATGATGGTGATCATGCT@@@@@@C@@C@C@@CCCCC@@CC@CC7777832324NM:i:0MD:Z:36AS:i:36XS:i:36Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:1193:16038161chrIX18722036MchrIV15296350NAAGTAAATTTACGATCTGGAAGGAGTGCTGTATGT&,,,,22032@@@@@@@@@@@@@@@@@@@@@@@@@@NM:i:2MD:Z:0A11G23AS:i:30XS:i:30XA:Z:chrX,+18705,36M,2;chrXV,+24474,36M,2;Yt:Z:MM 54 HWUSI-EAS1533_0033_FC:1:1:1193:16038 ! 0 ! 0 - - MM HWUSI-EAS1533_0033_FC:1:1:1193:1603881chrIV1529635036MchrIX187220AATTGACATTAAGCAATTGATGATGGTGATCATGCT@@@@@@C@@C@C@@CCCCC@@CC@CC7777832324NM:i:0MD:Z:36AS:i:36XS:i:36Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:1193:16038161chrIX18722036MchrIV15296350NAAGTAAATTTACGATCTGGAAGGAGTGCTGTATGT&,,,,22032@@@@@@@@@@@@@@@@@@@@@@@@@@NM:i:2MD:Z:0A11G23AS:i:30XS:i:30XA:Z:chrX,+18705,36M,2;chrXV,+24474,36M,2;Yt:Z:MM
55 HWUSI-EAS1533_0033_FC:1:1:2292:14294 ! 0 ! 0 - - MM HWUSI-EAS1533_0033_FC:1:1:2292:1429481chrVII1001809036M=1001598-247ATCGAAGATCCATTTGCTGAAGATGACTGGGAAGCT7@@@@@C@@@C@C@CC@@@@C@C@C@778771111-NM:i:0MD:Z:36AS:i:36XS:i:36XA:Z:chrVIII,-452209,36M,0;Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:2292:14294161chrVII1001598036M=1001809247NGCTTTGGACTTGATTGTTGACGCTATCAAGGCTGC)333377777@C@@@C@CCC@@@@C@C@@CC@@@@@NM:i:1MD:Z:0A35AS:i:35XS:i:35XA:Z:chrVIII,+451998,36M,1;Yt:Z:MM 55 HWUSI-EAS1533_0033_FC:1:1:2292:14294 ! 0 ! 0 - - MM HWUSI-EAS1533_0033_FC:1:1:2292:1429481chrVII1001809036M=1001598-247ATCGAAGATCCATTTGCTGAAGATGACTGGGAAGCT7@@@@@C@@@C@C@CC@@@@C@C@C@778771111-NM:i:0MD:Z:36AS:i:36XS:i:36XA:Z:chrVIII,-452209,36M,0;Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:2292:14294161chrVII1001598036M=1001809247NGCTTTGGACTTGATTGTTGACGCTATCAAGGCTGC)333377777@C@@@C@CCC@@@@C@C@@CC@@@@@NM:i:1MD:Z:0A35AS:i:35XS:i:35XA:Z:chrVIII,+451998,36M,1;Yt:Z:MM
56 HWUSI-EAS1533_0033_FC:1:1:1843:8071 ! 0 ! 0 - - MM HWUSI-EAS1533_0033_FC:1:1:1843:807181chrX11499036M=180736540ATTATTTGGGTATTCCTACTCATTCCACTGTCCAAT208488@@@@@@@@@@@@5@@@@@@@20122++,0+NM:i:0MD:Z:36AS:i:36XS:i:36XA:Z:chrIX,-11516,36M,0;Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:1843:8071161chrX18073036M=11499-6540NAATTGTTTGGAGGAATTGGCTTGCCTTCGGCGTCA&.)*)//3,*@@@@@<<5<<<<<7:@@@@@@@@@@@NM:i:1MD:Z:0C35AS:i:35XS:i:35XA:Z:chrXV,+23831,36M,1;chrVII,-1077024,36M,1;chrVII,+1068528,36M,1;chrIX,+18090,36M,1;chrII,-805776,36M,1;Yt:Z:MM 56 HWUSI-EAS1533_0033_FC:1:1:1843:8071 ! 0 ! 0 - - MM HWUSI-EAS1533_0033_FC:1:1:1843:807181chrX11499036M=180736540ATTATTTGGGTATTCCTACTCATTCCACTGTCCAAT208488@@@@@@@@@@@@5@@@@@@@20122++,0+NM:i:0MD:Z:36AS:i:36XS:i:36XA:Z:chrIX,-11516,36M,0;Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:1843:8071161chrX18073036M=11499-6540NAATTGTTTGGAGGAATTGGCTTGCCTTCGGCGTCA&.)*)//3,*@@@@@<<5<<<<<7:@@@@@@@@@@@NM:i:1MD:Z:0C35AS:i:35XS:i:35XA:Z:chrXV,+23831,36M,1;chrVII,-1077024,36M,1;chrVII,+1068528,36M,1;chrIX,+18090,36M,1;chrII,-805776,36M,1;Yt:Z:MM
57 HWUSI-EAS1533_0033_FC:1:1:2050:8363 ! 0 ! 0 - - MM HWUSI-EAS1533_0033_FC:1:1:2050:836381chrX729768036M=729583-221CACTTTACATAACCTGGATAAGTAATATTTCAAGCT@@@@@@CC@@C@@@@@@@CCC@CC@@77777-..2,NM:i:2MD:Z:2T32C0AS:i:32XS:i:32XA:Z:chrIV,+15997,36M,2;Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:2050:8363161chrX729583036M=729768221NTGTCTGTAGACATAGCTTGGAAGTATGTGTATTGT'//..77877@CCC@@CCCCC@@C@@@@@@@@CC@@NM:i:1MD:Z:0T35AS:i:35XS:i:35XA:Z:chrIV,-16182,36M,1;Yt:Z:MM 57 HWUSI-EAS1533_0033_FC:1:1:2050:8363 ! 0 ! 0 - - MM HWUSI-EAS1533_0033_FC:1:1:2050:836381chrX729768036M=729583-221CACTTTACATAACCTGGATAAGTAATATTTCAAGCT@@@@@@CC@@C@@@@@@@CCC@CC@@77777-..2,NM:i:2MD:Z:2T32C0AS:i:32XS:i:32XA:Z:chrIV,+15997,36M,2;Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:2050:8363161chrX729583036M=729768221NTGTCTGTAGACATAGCTTGGAAGTATGTGTATTGT'//..77877@CCC@@CCCCC@@C@@@@@@@@CC@@NM:i:1MD:Z:0T35AS:i:35XS:i:35XA:Z:chrIV,-16182,36M,1;Yt:Z:MM