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planemo upload for repository https://github.com/open2c/pairtools commit e9ebcf7ac032fafaa445e654b245df679a4bbf18
author iuc
date Thu, 04 Apr 2024 19:40:36 +0000
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## pairs format v1.0.0
#sorted: chr1-chr2-pos1-pos2
#shape: upper triangle
#genome_assembly: unknown
#chromsize: chrI 230218
#chromsize: chrII 813184
#chromsize: chrIII 316620
#chromsize: chrIV 1531933
#chromsize: chrV 576874
#chromsize: chrVI 270161
#chromsize: chrVII 1090940
#chromsize: chrVIII 562643
#chromsize: chrIX 439888
#chromsize: chrX 745751
#chromsize: chrXI 666816
#chromsize: chrXII 1078177
#chromsize: chrXIII 924431
#chromsize: chrXIV 784333
#chromsize: chrXV 1091291
#chromsize: chrXVI 948066
#chromsize: chrM 85779
#samheader: @SQ	SN:chrI	LN:230218
#samheader: @SQ	SN:chrII	LN:813184
#samheader: @SQ	SN:chrIII	LN:316620
#samheader: @SQ	SN:chrIV	LN:1531933
#samheader: @SQ	SN:chrIX	LN:439888
#samheader: @SQ	SN:chrM	LN:85779
#samheader: @SQ	SN:chrV	LN:576874
#samheader: @SQ	SN:chrVI	LN:270161
#samheader: @SQ	SN:chrVII	LN:1090940
#samheader: @SQ	SN:chrVIII	LN:562643
#samheader: @SQ	SN:chrX	LN:745751
#samheader: @SQ	SN:chrXI	LN:666816
#samheader: @SQ	SN:chrXII	LN:1078177
#samheader: @SQ	SN:chrXIII	LN:924431
#samheader: @SQ	SN:chrXIV	LN:784333
#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:/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_markdups.pairsam --output-dups output_dups_pairs_markdups.pairsam --mark-dups output_sorted_pairs.pairsam	PP:pairtools_sort-1.3	VN:1.0.2
#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_markdups.pairsam --output-dups output_dups_pairs_markdups.pairsam --mark-dups output_sorted_pairs.pairsam	PP:pairtools_sort-2.3	VN:1.0.2
#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_markdups.pairsam --output-dups output_dups_pairs_markdups.pairsam --mark-dups output_sorted_pairs.pairsam	PP:pairtools_sort-3.3	VN:1.0.2
#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_markdups.pairsam --output-dups output_dups_pairs_markdups.pairsam --mark-dups output_sorted_pairs.pairsam	PP:pairtools_sort-4.4	VN:1.0.2
#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2
HWI-ST560:29:B0A7LABXX:2:1101:2692:4382	chrIII	80421	chrIII	80656	+	-	DD	HWI-ST560:29:B0A7LABXX:2:1101:2692:4382161chrIII804216050M=80607236CTCTTCTAGCAGGAAGAGATCGTCCTTTTTACTGTCCTCGAATCCTACCGCCCFFFFFHHHHHGIIGIGIJIIJJJJJJJJIJJIJJIJJJIJIIFIJIINM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU	HWI-ST560:29:B0A7LABXX:2:1101:2692:438281chrIII806076050M=80421-236ATCTTATATGCCTAATACAAAAAGAAGCTCACTAACATCAAAATCATTATHIGGFIIGIIJJJJJIHJJJJHHFIJJIHIFIJJJHGCC>332224D=:1NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU
HWUSI-EAS1533_0033_FC:1:1:2403:20808	chrIV	497939	chrIV	498215	+	-	DD	HWUSI-EAS1533_0033_FC:1:1:2403:2080897chrIV4979396036M=498180277CGCTTTCATTACTCGAATCCGTCAAAGACGCTTCTT4544588888C@@CC@CCC@@@C@@@C@CCC@C@CCNM:i:1MD:Z:0A35AS:i:35XS:i:0Yt:Z:UU	HWUSI-EAS1533_0033_FC:1:1:2403:20808145chrIV4981806036M=497939-277GGCTGGTGAAGGAGTATTATTTACAATTCTAAAGCN@@C@@@@CC@CC@CC22C@@@CCCCC888886666)NM:i:1MD:Z:35T0AS:i:35XS:i:0Yt:Z:UU
HWI-ST560:29:B0A7LABXX:2:1101:20583:3832	chrIV	623680	chrIV	623930	+	-	DD	HWI-ST560:29:B0A7LABXX:2:1101:20583:3832161chrIV6236806050M=623881251TAAACAGTTAATGAAATCAGTTGTTACAAATGAGTTTCAATGCAGCTTAABBCFDFDDHHFCHGIII<ABHHHHIHFHFDGIIIIJJJJJGIIDHICGGGNM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU	HWI-ST560:29:B0A7LABXX:2:1101:20583:383281chrIV6238814450M=623680-251GGATCATCTAGATGAAGAGTTGGACCTGACTGGGCCGATAAACAACTCACB909DHD?F?*?*GHFF???:*11IHHFAFFGFGC<23233322244141NM:i:3MD:Z:5G6G8T28AS:i:35XS:i:0Yt:Z:UU
HWI-ST560:29:B0A7LABXX:2:1101:21049:12870	chrVII	395112	chrVII	395330	+	-	DD	HWI-ST560:29:B0A7LABXX:2:1101:21049:1287097chrVII395112603S47M=395298219AAATTTTATCATAAAGATGAAAAACCTCGACCACGTTTTGCACATCAGCA##################################################NM:i:3MD:Z:9C9C4T22AS:i:32XS:i:0Yt:Z:UU	HWI-ST560:29:B0A7LABXX:2:1101:21049:12870145chrVII3952986017S33M=395112-219TCGAAGGTAGACATCTTACTTGTAGTACCACAACTGAATGAAATCTTGCT####################EHDC4A3EA<3<,,9<?4C2:+3A8DD@<=NM:i:0MD:Z:33AS:i:33XS:i:0Yt:Z:UU
HWUSI-EAS1533_0033_FC:1:1:2739:11140	chrVIII	403630	chrVIII	403904	+	-	DD	HWUSI-EAS1533_0033_FC:1:1:2739:11140161chrVIII4036305836M=403869275NGCTTGCTACTTTGTGCGAGCTTGATATGCAGGACA(22/277777C@CCCCC@@CCC@@C@@@CC@@@@@CNM:i:2MD:Z:0A15T19AS:i:30XS:i:0Yt:Z:UU	HWUSI-EAS1533_0033_FC:1:1:2739:1114081chrVIII4038696036M=403630-275AGTTTTTCTGACGATCTGAAGTCTGTTTACCAAGCA@444CCCC@@CC@@@CC@CCCCCCCC877773333=NM:i:1MD:Z:35T0AS:i:35XS:i:0Yt:Z:UU
HWI-ST560:29:B0A7LABXX:2:1101:20782:17358	chrXIII	538121	chrXIII	544653	-	-	DD	HWI-ST560:29:B0A7LABXX:2:1101:20782:17358177chrXIII5380726050M=5446046533GAGCTTCATCGGATGTTGGTGAGTGATGAATATCACGGTAAAGAATACAA3HEGED86)6GGHCHGDC2A<AEHA<<AHGHHDC1HHDHD?FAFDB=@@BNM:i:1MD:Z:0A49AS:i:49XS:i:0Yt:Z:UU	HWI-ST560:29:B0A7LABXX:2:1101:20782:17358113chrXIII5446046050M=538072-6533TATTGCGCTGACTTCGTTATCATTCAAGCTAACTAGTTCTTCCTCGTCTGAFGAGEGHF?0=HGFDB<CC4:1)FIIHGFF<C<2222230000044111NM:i:1MD:Z:23G26AS:i:45XS:i:0Yt:Z:UU
HWUSI-EAS1533_0033_FC:1:1:1306:18143	chrXIII	794677	chrXIII	794956	+	-	DD	HWUSI-EAS1533_0033_FC:1:1:1306:18143161chrXIII7946776036M=794921280NAGGTGGCAGCATAGCACTGTAATGAGATATATTAA%&(&)*)*+,:1:::<<<:0::3::@@@5@@@:@@@NM:i:1MD:Z:0G35AS:i:35XS:i:0Yt:Z:UU	HWUSI-EAS1533_0033_FC:1:1:1306:1814381chrXIII7949216036M=794677-280GGCTAGGCCAGTTAATACAAACGCTGAAACGGAATG####################################NM:i:1MD:Z:35C0AS:i:35XS:i:0Yt:Z:UU
HWI-ST560:29:B0A7LABXX:2:1101:19177:20440	chrXV	1012747	chrXV	1012994	+	-	DD	HWI-ST560:29:B0A7LABXX:2:1101:19177:2044097chrXV10127476050M=1012945248GATCTGCTTATTAAATCTGGCATAATAAAGTTGATTGTCTTGACGTTGCA11+44224222222<C<AEI:CBEIGIBH><FCHIBFHGHIGIII8?FFHNM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU	HWI-ST560:29:B0A7LABXX:2:1101:19177:20440145chrXV10129456050M=1012747-248AACTTTTAACTCGGGAAATATGTATCACTATACTAAAAAACATTAATTTABFIGGGIIGGG@CBCFBCHHIHHH@FF<DF<FFE?DAHFCFA+?DBD@@?NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU
HWI-ST560:29:B0A7LABXX:2:1101:15890:13657	chrXVI	416774	chrXVI	486947	-	-	DD	HWI-ST560:29:B0A7LABXX:2:1101:15890:13657113chrXVI4167255150M=48689870174AGGGAGTAACAACGGATCGCAGTCAAATGAACTTCAGATACGGTATAAGC#######?9?93???@/@?<>)<@>=>89933).@?=22202))222000NM:i:3MD:Z:2T18T20T7AS:i:37XS:i:0Yt:Z:UU	HWI-ST560:29:B0A7LABXX:2:1101:15890:13657177chrXVI4868984850M=416725-70174GAGAAACTTTTCATCAAAGCTAAAAGGCACTCACACAAGCCTTCCCGTCCB8BD>BF?*D>D?<GCG?*)@@IGBC*?1C1C2FAAGDDF<))DDA+=B=NM:i:3MD:Z:19A6T19T3AS:i:36XS:i:0Yt:Z:UU