diff test-data/output_parsed_pairs_bam_5unique.pairs @ 2:6cbca5661205 draft

planemo upload for repository https://github.com/open2c/pairtools commit 162c595b19e442f40be4c2f5434b20b56ade52d4
author iuc
date Tue, 30 Apr 2024 12:02:01 +0000 (10 months ago)
parents 3c87fa1a3b50
children c20a07c9237b
line wrap: on
line diff
--- a/test-data/output_parsed_pairs_bam_5unique.pairs	Tue Apr 16 12:50:25 2024 +0000
+++ b/test-data/output_parsed_pairs_bam_5unique.pairs	Tue Apr 30 12:02:01 2024 +0000
@@ -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