Mercurial > repos > iuc > pairtools_stats
diff test-data/output_dups_pairs_markdups.pairsam @ 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 |
| parents | 3c87fa1a3b50 |
| children |
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--- a/test-data/output_dups_pairs_markdups.pairsam Tue Apr 16 12:50:25 2024 +0000 +++ b/test-data/output_dups_pairs_markdups.pairsam Tue Apr 30 12:02:01 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_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:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --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_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:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --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_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:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --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_markdups.pairsam --output-dups output_dups_pairs_markdups.pairsam --mark-dups 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/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --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:2:1101:2692:4382 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