Mercurial > repos > iuc > pairtools_split

diff test-data/output_dedup_pairs.pairsam @ 3:060f0fed864e draft

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planemo upload for repository https://github.com/open2c/pairtools commit 162c595b19e442f40be4c2f5434b20b56ade52d4
author iuc
date Tue, 30 Apr 2024 12:02:15 +0000
parents bffcba7ce9b5
children
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--- a/test-data/output_dedup_pairs.pairsam	Tue Apr 16 12:50:54 2024 +0000
+++ b/test-data/output_dedup_pairs.pairsam	Tue Apr 30 12:02:15 2024 +0000
@@ -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