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Changeset 5:56bb29747b4d (2024-05-21)

Previous changeset 4:55a53b5e308d (2024-04-30) Next changeset 6:0bc216235d4c (2024-12-22)

Commit message:
planemo upload for repository https://github.com/open2c/pairtools commit 13aa776596c927adff29d936740ac80f0e37375d

modified:
macros.xml
test-data/output_dedup_sorted.pairsam
test-data/output_parsed_pairs_bam.pairs
test-data/output_parsed_pairs_bam_5unique.pairs
test-data/output_parsed_pairs_bam_min_mapq_40.pairs
test-data/output_parsed_pairs_bam_readid_dropped.pairs
test-data/output_parsed_pairs_bam_readid_dropped_seq.pairs
test-data/output_parsed_pairs_sam.pairs
test-data/output_parsed_pairs_sam_assemblyname.pairs
test-data/output_sorted_pairs.pairs

diff -r 55a53b5e308d -r 56bb29747b4d macros.xml
--- a/macros.xml Tue Apr 30 12:02:29 2024 +0000
+++ b/macros.xml Tue May 21 16:03:55 2024 +0000

@@ -1,6 +1,6 @@
<macros>
     <token name="@TOOL_VERSION@">1.1.0</token>
-    <token name="@SUFFIX_VERSION@">0</token>
+    <token name="@SUFFIX_VERSION@">1</token>
     <xml name="edam_ontology">
         <edam_datas>
             <edam_data>topic_1381</edam_data>

diff -r 55a53b5e308d -r 56bb29747b4d test-data/output_dedup_sorted.pairsam
--- a/test-data/output_dedup_sorted.pairsam Tue Apr 30 12:02:29 2024 +0000
+++ b/test-data/output_dedup_sorted.pairsam Tue May 21 16:03:55 2024 +0000

b'@@ -40,23 +40,23 @@\n #samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/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\tPP:bwa\tVN:1.0.2\n #samheader: @PG\tID:pairtools_sort-1.3\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-1.2\tVN:1.0.2\n #samheader: @PG\tID:pairtools_dedup-1.4\tPN:pairtools_dedup\tCL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-1.3\tVN:1.1.0\n-#samheader: @PG\tID:pairtools_sort-1.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-1.4\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-1.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpcoq066hp/files/6/5/3/dataset_65373f5c-e37e-4bba-ad0c-bd994c7eb46d.dat -o /tmp/tmpcoq066hp/job_working_directory/000/4/outputs/dataset_61b2dd7e-1796-45d8-9570-dba69c253aed.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-1.4\tVN:1.1.0\n #samheader: @PG\tID:bwa-2CCE5976\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz\n #samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/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\tPP:bwa-2CCE5976\tVN:1.0.2\n #samheader: @PG\tID:pairtools_sort-2.3\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-2.2\tVN:1.0.2\n #samheader: @PG\tID:pairtools_dedup-2.4\tPN:pairtools_dedup\tCL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-2.3\tVN:1.1.0\n-#samheader: @PG\tID:pairtools_sort-2.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-2.4\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-2.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpcoq066hp/files/6/5/3/dataset_65373f5c-e37e-4bba-ad0c-bd994c7eb46d.dat -o /tmp/tmpcoq066hp/job_working_directory/000/4/outputs/dataset_61b2dd7e-1796-45d8-9570-dba69c253aed.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-2.4\tVN:1.1.0\n #samheader: @PG\tID:bwa-3CAFD9D9\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz\n #samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/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.red'..b'v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-3.3\tVN:1.1.0\n-#samheader: @PG\tID:pairtools_sort-3.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-3.4\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-3.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpcoq066hp/files/6/5/3/dataset_65373f5c-e37e-4bba-ad0c-bd994c7eb46d.dat -o /tmp/tmpcoq066hp/job_working_directory/000/4/outputs/dataset_61b2dd7e-1796-45d8-9570-dba69c253aed.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-3.4\tVN:1.1.0\n #samheader: @PG\tID:bwa-4548A671\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz\n #samheader: @PG\tID:samtools\tPN:samtools\tPP:bwa-4548A671\tVN:1.19.2\tCL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam\n #samheader: @PG\tID:pairtools_parse-4.3\tPN:pairtools_parse\tCL:/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\tPP:samtools\tVN:1.0.2\n #samheader: @PG\tID:pairtools_sort-4.4\tPN:pairtools_sort\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs\tPP:pairtools_parse-4.3\tVN:1.0.2\n #samheader: @PG\tID:pairtools_dedup-4.5\tPN:pairtools_dedup\tCL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_sort-4.4\tVN:1.1.0\n-#samheader: @PG\tID:pairtools_sort-4.6\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-4.5\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-4.6\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpcoq066hp/files/6/5/3/dataset_65373f5c-e37e-4bba-ad0c-bd994c7eb46d.dat -o /tmp/tmpcoq066hp/job_working_directory/000/4/outputs/dataset_61b2dd7e-1796-45d8-9570-dba69c253aed.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-4.5\tVN:1.1.0\n #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2\n HWI-ST560:29:B0A7LABXX:2:1101:15566:24141\tchrI\t3199\tchrI\t3399\t+\t-\tUU\tHWI-ST560:29:B0A7LABXX:2:1101:15566:24141\x1997\x19chrI\x193199\x1960\x1915S35M\x19=\x193350\x19201\x19CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA\x19111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FH\x19NM:i:0\x19MD:Z:35\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:15566:24141\x19145\x19chrI\x193350\x1960\x1950M\x19=\x193199\x19-201\x19TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATC\x19GHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==\x19NM:i:0\x19MD:Z:50\x19AS:i:50\x19XS:i:0\x19Yt:Z:UU\n HWI-ST560:29:B0A7LABXX:2:1101:18861:21891\tchrI\t35431\tchrI\t35703\t+\t-\tUU\tHWI-ST560:29:B0A7LABXX:2:1101:18861:21891\x1997\x19chrI\x1935431\x1960\x1950M\x19=\x1935654\x19273\x19GACCACGTGGTCGTTGATGCTGCCAGCAGTTGTGCAGACCTGCATTGCTG\x19114442222322<2@FEAFHFH<CFHFFH?GH:CDHGGIGEFDG<BBH9?\x19NM:i:1\x19MD:Z:35G14\x19AS:i:45\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:18861:21891\x19145\x19chrI\x1935654\x1960\x1950M\x19=\x1935431\x19-273\x19ATGTGGCTGCTTTAATTGAGCCTCTTTCTGTCACCTGGCATGCTGTTAAG\x19>EGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFD<HFFDDDDB@B\x19NM:i:1\x19MD:Z:14G35\x19AS:i:45\x19XS:i:0\x19Yt:Z:UU\n'

diff -r 55a53b5e308d -r 56bb29747b4d test-data/output_parsed_pairs_bam.pairs
--- a/test-data/output_parsed_pairs_bam.pairs Tue Apr 30 12:02:29 2024 +0000
+++ b/test-data/output_parsed_pairs_bam.pairs Tue May 21 16:03:55 2024 +0000

b'@@ -18,7 +18,7 @@\n #chromsize: chrXV 1091291\n #chromsize: chrXVI 948066\n #chromsize: chrM 85779\n-#samheader: @HD\tVN:1.6\tSO:coordinate\n+#samheader: @HD\tVN:1.6\tSO:queryname\n #samheader: @SQ\tSN:chrI\tLN:230218\n #samheader: @SQ\tSN:chrII\tLN:813184\n #samheader: @SQ\tSN:chrIII\tLN:316620\n@@ -37,2467 +37,2004 @@\n #samheader: @SQ\tSN:chrXV\tLN:1091291\n #samheader: @SQ\tSN:chrXVI\tLN:948066\n #samheader: @PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/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\tPP:bwa\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/3/a/6/dataset_3a6251e3-16fc-4685-babe-d12b42999e62.dat -c /tmp/tmprvti6kw7/files/5/6/2/dataset_562f805b-59bf-489a-8b58-f6e996bc1d69.dat -o /tmp/tmprvti6kw7/job_working_directory/000/7/outputs/dataset_3f99deff-4f79-499c-b1a1-93c99ce1de58.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa\tVN:1.1.0\n #samheader: @PG\tID:bwa-2CCE5976\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/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\tPP:bwa-2CCE5976\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/3/a/6/dataset_3a6251e3-16fc-4685-babe-d12b42999e62.dat -c /tmp/tmprvti6kw7/files/5/6/2/dataset_562f805b-59bf-489a-8b58-f6e996bc1d69.dat -o /tmp/tmprvti6kw7/job_working_directory/000/7/outputs/dataset_3f99deff-4f79-499c-b1a1-93c99ce1de58.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-2CCE5976\tVN:1.1.0\n #samheader: @PG\tID:bwa-3CAFD9D9\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/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\tPP:bwa-3CAFD9D9\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/3/a/6/dataset_3a6251e3-16fc-4685-babe-d12b42999e62.dat -c /tmp/tmprvti6kw7/files/5/6/2/dataset_562f805b-59bf-489a-8b58-f6e996bc1d69.dat -o /tmp/tmprvti6kw7/job_working_directory/000/7/outputs/dataset_3f99deff-4f79-499c-b1a1-93c99ce1de58.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-3CAFD9D9\tVN:1.1.0\n #samheader: @PG\tID:bwa-4548A671\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz\n #samheader: @PG\tID:samtools\tPN:samtools\tPP:bwa-4548A671\tVN:1.19.2\t'..b"62\x1960\x1936M\x19=\x1959346\x1916785\x19ATTAAAAATATTAATAAAATTATTATTATTTAATCT\x19CC222CCC@@@222@@CCC@CCC@22899995445-\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:21\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3045:13383\x19177\x19chrM\x1959346\x1960\x1936M\x19=\x1942562\x19-16785\x19TAGGTTTAACTATAAAAGTACGGCCCCTAATTAAAN\x19C@@@@@@CC@44CCCCCCCCCCCCCC787773333)\x19NM:i:2\x19MD:Z:0A34T0\x19AS:i:34\x19XS:i:0\x19Yt:Z:UU\n HWUSI-EAS1533_0033_FC:1:1:3045:15943\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3045:15943\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19,,,,,33853@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3045:15943\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&*,0*22220@@C@@@@@@@@@@@@C@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:3047:2837\tchrVIII\t403054\tchrVIII\t403360\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3047:2837\x1997\x19chrVIII\x19403054\x1960\x1936M\x19=\x19403325\x19307\x19CGCTTTTGATGGATAATTCATGCAATAACTGTCAAA\x19?323387778C@@@@@@@@@@@@@@@@@@C@C@CC@\x19NM:i:1\x19MD:Z:0A35\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3047:2837\x19145\x19chrVIII\x19403325\x1960\x1936M\x19=\x19403054\x19-307\x19TTTGCTCCGAGACTGTCAAGTATATATTTCCAAAAN\x19@@C@@@@CCCC@@C@CCCC@@CCCCC777773133)\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3050:10004\tchrXII\t999948\tchrXII\t1000205\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3050:10004\x1997\x19chrXII\x19999948\x1960\x1936M\x19=\x191000170\x19258\x19CCCATCCGCAAGACAGCTATCCTGCTGAGGCAGAAG\x19=311388777C@CCC@CCC@C@@@@@C@CCC@@@C@\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3050:10004\x19145\x19chrXII\x191000170\x1960\x1936M\x19=\x19999948\x19-258\x19TTGGTGTATACATTTATATTGAATTTAATAGCAACN\x19@C@@@@@@@@CCCCC@@CCC@C@CC@888883333)\x19NM:i:1\x19MD:Z:35A0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3052:7878\tchrII\t329706\tchrII\t396585\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3052:7878\x19177\x19chrII\x19329671\x1960\x1936M\x19=\x19396550\x1966880\x19TTGTCTGGTTTGTCCAGATTATCTGACACAGACTTN\x19@C@@@@C@C@C@@@CCCC@CC@@C@C55556.---'\x19NM:i:1\x19MD:Z:35T0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3052:7878\x19113\x19chrII\x19396550\x1960\x1936M\x19=\x19329671\x19-66880\x19CATGTATGAAGCATTGTTGAAACTGTCAACATCGTT\x19@C@C@CCCCCCC@CC@CCCCCCC@CC668661112-\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3055:11451\tchrVII\t706721\tchrIX\t216502\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3055:11451\x19113\x19chrVII\x19706691\x1960\x1931M5S\x19chrIX\x19216467\x190\x19AAGGTAATCAATGTGCTAAAACGGTAAATATCTAAG\x19CCCCCCCC@CCCC@CC@CC@CCCCCC58455//22:\x19NM:i:0\x19MD:Z:31\x19AS:i:31\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3055:11451\x19177\x19chrIX\x19216467\x1958\x1936M\x19chrVII\x19706691\x190\x19GTATCCAGCGTCTTCAATGGGATAAAGATATTCTAN\x19@@C@CCC@C@@@@@CC@C@CCCCCCC888883333)\x19NM:i:2\x19MD:Z:4G30T0\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3055:13807\tchrIV\t1436146\tchrIV\t1436437\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3055:13807\x19161\x19chrIV\x191436146\x1958\x1936M\x19=\x191436402\x19292\x19NTATATTTTTCGGTACGCTTGCGTTTCACTGGAGAG\x19'33/.888002@1@@@@@@@@@@@@@@@@@@@@@@@\x19NM:i:2\x19MD:Z:0T30A4\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3055:13807\x1981\x19chrIV\x191436402\x1960\x1936M\x19=\x191436146\x19-292\x19TTTTTTGAGACGAAACCTGGTTCAGGGCAAAAAGGT\x192CCC@CCC@@@@@CCCC@CC@CCCCC988896666-\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3057:5914\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B233366663@@@@@@C@C@@@@@@C@@@@@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&--//55333<:<<<:::::@@@@@<<<<<<<<<<@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n HWUSI-EAS1533_0033_FC:1:1:3057:21304\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:21304\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19AATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x194////66663@@C@@CC@@C@@@C@@C@CC@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:21304\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&----21512@@@@@<:<<<@@@@@:<::<::::::\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n-HWUSI-EAS1533_0033_FC:1:1:3057:5914\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B233366663@@@@@@C@C@@@@@@C@@@@@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&--//55333<:<<<:::::@@@@@<<<<<<<<<<@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n"

diff -r 55a53b5e308d -r 56bb29747b4d test-data/output_parsed_pairs_bam_5unique.pairs
--- a/test-data/output_parsed_pairs_bam_5unique.pairs Tue Apr 30 12:02:29 2024 +0000
+++ b/test-data/output_parsed_pairs_bam_5unique.pairs Tue May 21 16:03:55 2024 +0000

b'@@ -18,7 +18,7 @@\n #chromsize: chrXV 1091291\n #chromsize: chrXVI 948066\n #chromsize: chrM 85779\n-#samheader: @HD\tVN:1.6\tSO:coordinate\n+#samheader: @HD\tVN:1.6\tSO:queryname\n #samheader: @SQ\tSN:chrI\tLN:230218\n #samheader: @SQ\tSN:chrII\tLN:813184\n #samheader: @SQ\tSN:chrIII\tLN:316620\n@@ -37,2467 +37,2004 @@\n #samheader: @SQ\tSN:chrXV\tLN:1091291\n #samheader: @SQ\tSN:chrXVI\tLN:948066\n #samheader: @PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/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\tPP:bwa\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/3/b/4/dataset_3b4c7f78-6a1c-45b5-88a6-0e4d638240ad.dat -c /tmp/tmprvti6kw7/files/1/1/2/dataset_112ee393-867c-49e6-9b74-04fa83c0f30f.dat -o /tmp/tmprvti6kw7/job_working_directory/000/15/outputs/dataset_7880eea1-01ef-4e91-bf90-5861039ae343.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa\tVN:1.1.0\n #samheader: @PG\tID:bwa-2CCE5976\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/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\tPP:bwa-2CCE5976\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/3/b/4/dataset_3b4c7f78-6a1c-45b5-88a6-0e4d638240ad.dat -c /tmp/tmprvti6kw7/files/1/1/2/dataset_112ee393-867c-49e6-9b74-04fa83c0f30f.dat -o /tmp/tmprvti6kw7/job_working_directory/000/15/outputs/dataset_7880eea1-01ef-4e91-bf90-5861039ae343.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-2CCE5976\tVN:1.1.0\n #samheader: @PG\tID:bwa-3CAFD9D9\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/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\tPP:bwa-3CAFD9D9\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/3/b/4/dataset_3b4c7f78-6a1c-45b5-88a6-0e4d638240ad.dat -c /tmp/tmprvti6kw7/files/1/1/2/dataset_112ee393-867c-49e6-9b74-04fa83c0f30f.dat -o /tmp/tmprvti6kw7/job_working_directory/000/15/outputs/dataset_7880eea1-01ef-4e91-bf90-5861039ae343.dat --min-mapq 40 --max-molecule-size 750 --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-3CAFD9D9\tVN:1.1.0\n #samheader: @PG\tID:bwa-4548A671\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz\n #samheader: @PG\tID:samtools\tPN:samto'..b"62\x1960\x1936M\x19=\x1959346\x1916785\x19ATTAAAAATATTAATAAAATTATTATTATTTAATCT\x19CC222CCC@@@222@@CCC@CCC@22899995445-\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:21\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3045:13383\x19177\x19chrM\x1959346\x1960\x1936M\x19=\x1942562\x19-16785\x19TAGGTTTAACTATAAAAGTACGGCCCCTAATTAAAN\x19C@@@@@@CC@44CCCCCCCCCCCCCC787773333)\x19NM:i:2\x19MD:Z:0A34T0\x19AS:i:34\x19XS:i:0\x19Yt:Z:UU\n HWUSI-EAS1533_0033_FC:1:1:3045:15943\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3045:15943\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19,,,,,33853@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3045:15943\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&*,0*22220@@C@@@@@@@@@@@@C@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:3047:2837\tchrVIII\t403054\tchrVIII\t403360\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3047:2837\x1997\x19chrVIII\x19403054\x1960\x1936M\x19=\x19403325\x19307\x19CGCTTTTGATGGATAATTCATGCAATAACTGTCAAA\x19?323387778C@@@@@@@@@@@@@@@@@@C@C@CC@\x19NM:i:1\x19MD:Z:0A35\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3047:2837\x19145\x19chrVIII\x19403325\x1960\x1936M\x19=\x19403054\x19-307\x19TTTGCTCCGAGACTGTCAAGTATATATTTCCAAAAN\x19@@C@@@@CCCC@@C@CCCC@@CCCCC777773133)\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3050:10004\tchrXII\t999948\tchrXII\t1000205\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3050:10004\x1997\x19chrXII\x19999948\x1960\x1936M\x19=\x191000170\x19258\x19CCCATCCGCAAGACAGCTATCCTGCTGAGGCAGAAG\x19=311388777C@CCC@CCC@C@@@@@C@CCC@@@C@\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3050:10004\x19145\x19chrXII\x191000170\x1960\x1936M\x19=\x19999948\x19-258\x19TTGGTGTATACATTTATATTGAATTTAATAGCAACN\x19@C@@@@@@@@CCCCC@@CCC@C@CC@888883333)\x19NM:i:1\x19MD:Z:35A0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3052:7878\tchrII\t329706\tchrII\t396585\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3052:7878\x19177\x19chrII\x19329671\x1960\x1936M\x19=\x19396550\x1966880\x19TTGTCTGGTTTGTCCAGATTATCTGACACAGACTTN\x19@C@@@@C@C@C@@@CCCC@CC@@C@C55556.---'\x19NM:i:1\x19MD:Z:35T0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3052:7878\x19113\x19chrII\x19396550\x1960\x1936M\x19=\x19329671\x19-66880\x19CATGTATGAAGCATTGTTGAAACTGTCAACATCGTT\x19@C@C@CCCCCCC@CC@CCCCCCC@CC668661112-\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3055:11451\tchrVII\t706721\tchrIX\t216502\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3055:11451\x19113\x19chrVII\x19706691\x1960\x1931M5S\x19chrIX\x19216467\x190\x19AAGGTAATCAATGTGCTAAAACGGTAAATATCTAAG\x19CCCCCCCC@CCCC@CC@CC@CCCCCC58455//22:\x19NM:i:0\x19MD:Z:31\x19AS:i:31\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3055:11451\x19177\x19chrIX\x19216467\x1958\x1936M\x19chrVII\x19706691\x190\x19GTATCCAGCGTCTTCAATGGGATAAAGATATTCTAN\x19@@C@CCC@C@@@@@CC@C@CCCCCCC888883333)\x19NM:i:2\x19MD:Z:4G30T0\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3055:13807\tchrIV\t1436146\tchrIV\t1436437\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3055:13807\x19161\x19chrIV\x191436146\x1958\x1936M\x19=\x191436402\x19292\x19NTATATTTTTCGGTACGCTTGCGTTTCACTGGAGAG\x19'33/.888002@1@@@@@@@@@@@@@@@@@@@@@@@\x19NM:i:2\x19MD:Z:0T30A4\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3055:13807\x1981\x19chrIV\x191436402\x1960\x1936M\x19=\x191436146\x19-292\x19TTTTTTGAGACGAAACCTGGTTCAGGGCAAAAAGGT\x192CCC@CCC@@@@@CCCC@CC@CCCCC988896666-\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3057:5914\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B233366663@@@@@@C@C@@@@@@C@@@@@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&--//55333<:<<<:::::@@@@@<<<<<<<<<<@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n HWUSI-EAS1533_0033_FC:1:1:3057:21304\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:21304\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19AATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x194////66663@@C@@CC@@C@@@C@@C@CC@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:21304\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&----21512@@@@@<:<<<@@@@@:<::<::::::\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n-HWUSI-EAS1533_0033_FC:1:1:3057:5914\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B233366663@@@@@@C@C@@@@@@C@@@@@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&--//55333<:<<<:::::@@@@@<<<<<<<<<<@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n"

diff -r 55a53b5e308d -r 56bb29747b4d test-data/output_parsed_pairs_bam_min_mapq_40.pairs
--- a/test-data/output_parsed_pairs_bam_min_mapq_40.pairs Tue Apr 30 12:02:29 2024 +0000
+++ b/test-data/output_parsed_pairs_bam_min_mapq_40.pairs Tue May 21 16:03:55 2024 +0000

b'@@ -18,7 +18,7 @@\n #chromsize: chrXV 1091291\n #chromsize: chrXVI 948066\n #chromsize: chrM 85779\n-#samheader: @HD\tVN:1.6\tSO:coordinate\n+#samheader: @HD\tVN:1.6\tSO:queryname\n #samheader: @SQ\tSN:chrI\tLN:230218\n #samheader: @SQ\tSN:chrII\tLN:813184\n #samheader: @SQ\tSN:chrIII\tLN:316620\n@@ -37,2467 +37,2004 @@\n #samheader: @SQ\tSN:chrXV\tLN:1091291\n #samheader: @SQ\tSN:chrXVI\tLN:948066\n #samheader: @PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/0/b/d/dataset_0bd6cbee-0544-44c1-ad81-dd3845446ce7.dat -c /tmp/tmpchj83off/files/2/2/2/dataset_222eb307-af6a-471a-9d1d-00eab6969a45.dat -o /tmp/tmpchj83off/job_working_directory/000/11/outputs/dataset_55fc9726-73b7-4f53-83da-da08e1fbe4b9.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/9/a/1/dataset_9a1f8a60-b429-46a2-bb44-5ab9ebdd4956.dat -c /tmp/tmprvti6kw7/files/8/8/b/dataset_88ba6293-ea03-4ed1-9778-851c9fb56b47.dat -o /tmp/tmprvti6kw7/job_working_directory/000/11/outputs/dataset_70aa4b06-559b-4cbc-bd3b-9c5ac460d715.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa\tVN:1.1.0\n #samheader: @PG\tID:bwa-2CCE5976\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/0/b/d/dataset_0bd6cbee-0544-44c1-ad81-dd3845446ce7.dat -c /tmp/tmpchj83off/files/2/2/2/dataset_222eb307-af6a-471a-9d1d-00eab6969a45.dat -o /tmp/tmpchj83off/job_working_directory/000/11/outputs/dataset_55fc9726-73b7-4f53-83da-da08e1fbe4b9.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-2CCE5976\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/9/a/1/dataset_9a1f8a60-b429-46a2-bb44-5ab9ebdd4956.dat -c /tmp/tmprvti6kw7/files/8/8/b/dataset_88ba6293-ea03-4ed1-9778-851c9fb56b47.dat -o /tmp/tmprvti6kw7/job_working_directory/000/11/outputs/dataset_70aa4b06-559b-4cbc-bd3b-9c5ac460d715.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-2CCE5976\tVN:1.1.0\n #samheader: @PG\tID:bwa-3CAFD9D9\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/0/b/d/dataset_0bd6cbee-0544-44c1-ad81-dd3845446ce7.dat -c /tmp/tmpchj83off/files/2/2/2/dataset_222eb307-af6a-471a-9d1d-00eab6969a45.dat -o /tmp/tmpchj83off/job_working_directory/000/11/outputs/dataset_55fc9726-73b7-4f53-83da-da08e1fbe4b9.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-3CAFD9D9\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/9/a/1/dataset_9a1f8a60-b429-46a2-bb44-5ab9ebdd4956.dat -c /tmp/tmprvti6kw7/files/8/8/b/dataset_88ba6293-ea03-4ed1-9778-851c9fb56b47.dat -o /tmp/tmprvti6kw7/job_working_directory/000/11/outputs/dataset_70aa4b06-559b-4cbc-bd3b-9c5ac460d715.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-3CAFD9D9\tVN:1.1.0\n #samheader: @PG\tID:bwa-4548A671\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz\n #samheader: @PG\tID:samtools\tPN:samtools\tPP:bwa-4548A67'..b"62\x1960\x1936M\x19=\x1959346\x1916785\x19ATTAAAAATATTAATAAAATTATTATTATTTAATCT\x19CC222CCC@@@222@@CCC@CCC@22899995445-\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:21\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3045:13383\x19177\x19chrM\x1959346\x1960\x1936M\x19=\x1942562\x19-16785\x19TAGGTTTAACTATAAAAGTACGGCCCCTAATTAAAN\x19C@@@@@@CC@44CCCCCCCCCCCCCC787773333)\x19NM:i:2\x19MD:Z:0A34T0\x19AS:i:34\x19XS:i:0\x19Yt:Z:UU\n HWUSI-EAS1533_0033_FC:1:1:3045:15943\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3045:15943\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19,,,,,33853@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3045:15943\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&*,0*22220@@C@@@@@@@@@@@@C@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:3047:2837\tchrVIII\t403054\tchrVIII\t403360\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3047:2837\x1997\x19chrVIII\x19403054\x1960\x1936M\x19=\x19403325\x19307\x19CGCTTTTGATGGATAATTCATGCAATAACTGTCAAA\x19?323387778C@@@@@@@@@@@@@@@@@@C@C@CC@\x19NM:i:1\x19MD:Z:0A35\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3047:2837\x19145\x19chrVIII\x19403325\x1960\x1936M\x19=\x19403054\x19-307\x19TTTGCTCCGAGACTGTCAAGTATATATTTCCAAAAN\x19@@C@@@@CCCC@@C@CCCC@@CCCCC777773133)\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3050:10004\tchrXII\t999948\tchrXII\t1000205\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3050:10004\x1997\x19chrXII\x19999948\x1960\x1936M\x19=\x191000170\x19258\x19CCCATCCGCAAGACAGCTATCCTGCTGAGGCAGAAG\x19=311388777C@CCC@CCC@C@@@@@C@CCC@@@C@\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3050:10004\x19145\x19chrXII\x191000170\x1960\x1936M\x19=\x19999948\x19-258\x19TTGGTGTATACATTTATATTGAATTTAATAGCAACN\x19@C@@@@@@@@CCCCC@@CCC@C@CC@888883333)\x19NM:i:1\x19MD:Z:35A0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3052:7878\tchrII\t329706\tchrII\t396585\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3052:7878\x19177\x19chrII\x19329671\x1960\x1936M\x19=\x19396550\x1966880\x19TTGTCTGGTTTGTCCAGATTATCTGACACAGACTTN\x19@C@@@@C@C@C@@@CCCC@CC@@C@C55556.---'\x19NM:i:1\x19MD:Z:35T0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3052:7878\x19113\x19chrII\x19396550\x1960\x1936M\x19=\x19329671\x19-66880\x19CATGTATGAAGCATTGTTGAAACTGTCAACATCGTT\x19@C@C@CCCCCCC@CC@CCCCCCC@CC668661112-\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3055:11451\tchrVII\t706721\tchrIX\t216502\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3055:11451\x19113\x19chrVII\x19706691\x1960\x1931M5S\x19chrIX\x19216467\x190\x19AAGGTAATCAATGTGCTAAAACGGTAAATATCTAAG\x19CCCCCCCC@CCCC@CC@CC@CCCCCC58455//22:\x19NM:i:0\x19MD:Z:31\x19AS:i:31\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3055:11451\x19177\x19chrIX\x19216467\x1958\x1936M\x19chrVII\x19706691\x190\x19GTATCCAGCGTCTTCAATGGGATAAAGATATTCTAN\x19@@C@CCC@C@@@@@CC@C@CCCCCCC888883333)\x19NM:i:2\x19MD:Z:4G30T0\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3055:13807\tchrIV\t1436146\tchrIV\t1436437\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3055:13807\x19161\x19chrIV\x191436146\x1958\x1936M\x19=\x191436402\x19292\x19NTATATTTTTCGGTACGCTTGCGTTTCACTGGAGAG\x19'33/.888002@1@@@@@@@@@@@@@@@@@@@@@@@\x19NM:i:2\x19MD:Z:0T30A4\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3055:13807\x1981\x19chrIV\x191436402\x1960\x1936M\x19=\x191436146\x19-292\x19TTTTTTGAGACGAAACCTGGTTCAGGGCAAAAAGGT\x192CCC@CCC@@@@@CCCC@CC@CCCCC988896666-\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:3057:5914\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B233366663@@@@@@C@C@@@@@@C@@@@@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&--//55333<:<<<:::::@@@@@<<<<<<<<<<@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n HWUSI-EAS1533_0033_FC:1:1:3057:21304\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:21304\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19AATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x194////66663@@C@@CC@@C@@@C@@C@CC@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:21304\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&----21512@@@@@<:<<<@@@@@:<::<::::::\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n-HWUSI-EAS1533_0033_FC:1:1:3057:5914\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B233366663@@@@@@C@C@@@@@@C@@@@@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&--//55333<:<<<:::::@@@@@<<<<<<<<<<@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n"

diff -r 55a53b5e308d -r 56bb29747b4d test-data/output_parsed_pairs_bam_readid_dropped.pairs
--- a/test-data/output_parsed_pairs_bam_readid_dropped.pairs Tue Apr 30 12:02:29 2024 +0000
+++ b/test-data/output_parsed_pairs_bam_readid_dropped.pairs Tue May 21 16:03:55 2024 +0000

b'@@ -18,7 +18,7 @@\n #chromsize: chrXV 1091291\n #chromsize: chrXVI 948066\n #chromsize: chrM 85779\n-#samheader: @HD\tVN:1.6\tSO:coordinate\n+#samheader: @HD\tVN:1.6\tSO:queryname\n #samheader: @SQ\tSN:chrI\tLN:230218\n #samheader: @SQ\tSN:chrII\tLN:813184\n #samheader: @SQ\tSN:chrIII\tLN:316620\n@@ -37,2467 +37,2004 @@\n #samheader: @SQ\tSN:chrXV\tLN:1091291\n #samheader: @SQ\tSN:chrXVI\tLN:948066\n #samheader: @PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/2/b/6/dataset_2b603561-f23a-44dd-92b4-9db918b88c03.dat -c /tmp/tmpchj83off/files/1/b/6/dataset_1b6c0c8f-df3e-40c0-9161-19d29b52573a.dat -o /tmp/tmpchj83off/job_working_directory/000/19/outputs/dataset_272af137-1fda-4769-b54c-23281e79fcd4.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/0/2/c/dataset_02cedd3b-24df-4d7d-87c6-341b289f583b.dat -c /tmp/tmprvti6kw7/files/2/3/3/dataset_2334ea4f-3382-4441-a775-99e774623428.dat -o /tmp/tmprvti6kw7/job_working_directory/000/19/outputs/dataset_a095e2cc-7818-419d-b54e-cc5abff390a1.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa\tVN:1.1.0\n #samheader: @PG\tID:bwa-2CCE5976\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/2/b/6/dataset_2b603561-f23a-44dd-92b4-9db918b88c03.dat -c /tmp/tmpchj83off/files/1/b/6/dataset_1b6c0c8f-df3e-40c0-9161-19d29b52573a.dat -o /tmp/tmpchj83off/job_working_directory/000/19/outputs/dataset_272af137-1fda-4769-b54c-23281e79fcd4.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-2CCE5976\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/0/2/c/dataset_02cedd3b-24df-4d7d-87c6-341b289f583b.dat -c /tmp/tmprvti6kw7/files/2/3/3/dataset_2334ea4f-3382-4441-a775-99e774623428.dat -o /tmp/tmprvti6kw7/job_working_directory/000/19/outputs/dataset_a095e2cc-7818-419d-b54e-cc5abff390a1.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-2CCE5976\tVN:1.1.0\n #samheader: @PG\tID:bwa-3CAFD9D9\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/2/b/6/dataset_2b603561-f23a-44dd-92b4-9db918b88c03.dat -c /tmp/tmpchj83off/files/1/b/6/dataset_1b6c0c8f-df3e-40c0-9161-19d29b52573a.dat -o /tmp/tmpchj83off/job_working_directory/000/19/outputs/dataset_272af137-1fda-4769-b54c-23281e79fcd4.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-3CAFD9D9\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-3.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/0/2/c/dataset_02cedd3b-24df-4d7d-87c6-341b289f583b.dat -c /tmp/tmprvti6kw7/files/2/3/3/dataset_2334ea4f-3382-4441-a775-99e774623428.dat -o /tmp/tmprvti6kw7/job_working_directory/000/19/outputs/dataset_a095e2cc-7818-419d-b54e-cc5abff390a1.dat --min-mapq 40 --max-molecule-size 750 --drop-readid --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-3CAFD9D9\tVN:1.1.0\n #samheader: @PG\tID:bwa-4548A671\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2'..b"@@@CC@CCC@CC@@@CCC@CC2222\x19AS:i:0\x19XS:i:0\x19Yt:Z:NU\tHWUSI-EAS1533_0033_FC:1:1:3045:7969\x1973\x19chrIV\x1986211\x1960\x1936M\x19=\x1986211\x190\x19ACCTCATCAGAGGAGAGGTAATCGAGCAAGGGACCA\x194333177777CCC@@@@@@@@@@@@@@@@C@@CC@@\x19NM:i:1\x19MD:Z:0T35\x19AS:i:35\x19XS:i:0\x19Yt:Z:NU\n+.\tchrM\t42597\tchrM\t59381\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3045:13383\x19113\x19chrM\x1942562\x1960\x1936M\x19=\x1959346\x1916785\x19ATTAAAAATATTAATAAAATTATTATTATTTAATCT\x19CC222CCC@@@222@@CCC@CCC@22899995445-\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:21\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3045:13383\x19177\x19chrM\x1959346\x1960\x1936M\x19=\x1942562\x19-16785\x19TAGGTTTAACTATAAAAGTACGGCCCCTAATTAAAN\x19C@@@@@@CC@44CCCCCCCCCCCCCC787773333)\x19NM:i:2\x19MD:Z:0A34T0\x19AS:i:34\x19XS:i:0\x19Yt:Z:UU\n .\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3045:15943\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19,,,,,33853@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3045:15943\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&*,0*22220@@C@@@@@@@@@@@@C@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+.\tchrVIII\t403054\tchrVIII\t403360\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3047:2837\x1997\x19chrVIII\x19403054\x1960\x1936M\x19=\x19403325\x19307\x19CGCTTTTGATGGATAATTCATGCAATAACTGTCAAA\x19?323387778C@@@@@@@@@@@@@@@@@@C@C@CC@\x19NM:i:1\x19MD:Z:0A35\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3047:2837\x19145\x19chrVIII\x19403325\x1960\x1936M\x19=\x19403054\x19-307\x19TTTGCTCCGAGACTGTCAAGTATATATTTCCAAAAN\x19@@C@@@@CCCC@@C@CCCC@@CCCCC777773133)\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+.\tchrXII\t999948\tchrXII\t1000205\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3050:10004\x1997\x19chrXII\x19999948\x1960\x1936M\x19=\x191000170\x19258\x19CCCATCCGCAAGACAGCTATCCTGCTGAGGCAGAAG\x19=311388777C@CCC@CCC@C@@@@@C@CCC@@@C@\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3050:10004\x19145\x19chrXII\x191000170\x1960\x1936M\x19=\x19999948\x19-258\x19TTGGTGTATACATTTATATTGAATTTAATAGCAACN\x19@C@@@@@@@@CCCCC@@CCC@C@CC@888883333)\x19NM:i:1\x19MD:Z:35A0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+.\tchrII\t329706\tchrII\t396585\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3052:7878\x19177\x19chrII\x19329671\x1960\x1936M\x19=\x19396550\x1966880\x19TTGTCTGGTTTGTCCAGATTATCTGACACAGACTTN\x19@C@@@@C@C@C@@@CCCC@CC@@C@C55556.---'\x19NM:i:1\x19MD:Z:35T0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3052:7878\x19113\x19chrII\x19396550\x1960\x1936M\x19=\x19329671\x19-66880\x19CATGTATGAAGCATTGTTGAAACTGTCAACATCGTT\x19@C@C@CCCCCCC@CC@CCCCCCC@CC668661112-\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+.\tchrVII\t706721\tchrIX\t216502\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3055:11451\x19113\x19chrVII\x19706691\x1960\x1931M5S\x19chrIX\x19216467\x190\x19AAGGTAATCAATGTGCTAAAACGGTAAATATCTAAG\x19CCCCCCCC@CCCC@CC@CC@CCCCCC58455//22:\x19NM:i:0\x19MD:Z:31\x19AS:i:31\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3055:11451\x19177\x19chrIX\x19216467\x1958\x1936M\x19chrVII\x19706691\x190\x19GTATCCAGCGTCTTCAATGGGATAAAGATATTCTAN\x19@@C@CCC@C@@@@@CC@C@CCCCCCC888883333)\x19NM:i:2\x19MD:Z:4G30T0\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\n+.\tchrIV\t1436146\tchrIV\t1436437\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:3055:13807\x19161\x19chrIV\x191436146\x1958\x1936M\x19=\x191436402\x19292\x19NTATATTTTTCGGTACGCTTGCGTTTCACTGGAGAG\x19'33/.888002@1@@@@@@@@@@@@@@@@@@@@@@@\x19NM:i:2\x19MD:Z:0T30A4\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:3055:13807\x1981\x19chrIV\x191436402\x1960\x1936M\x19=\x191436146\x19-292\x19TTTTTTGAGACGAAACCTGGTTCAGGGCAAAAAGGT\x192CCC@CCC@@@@@CCCC@CC@CCCCC988896666-\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:0\x19Yt:Z:UU\n+.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B233366663@@@@@@C@C@@@@@@C@@@@@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&--//55333<:<<<:::::@@@@@<<<<<<<<<<@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n .\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:21304\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19AATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x194////66663@@C@@CC@@C@@@C@@C@CC@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:21304\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&----21512@@@@@<:<<<@@@@@:<::<::::::\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n-.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B233366663@@@@@@C@C@@@@@@C@@@@@@@C@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3057:5914\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&--//55333<:<<<:::::@@@@@<<<<<<<<<<@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n"

diff -r 55a53b5e308d -r 56bb29747b4d test-data/output_parsed_pairs_bam_readid_dropped_seq.pairs
--- a/test-data/output_parsed_pairs_bam_readid_dropped_seq.pairs Tue Apr 30 12:02:29 2024 +0000
+++ b/test-data/output_parsed_pairs_bam_readid_dropped_seq.pairs Tue May 21 16:03:55 2024 +0000

diff -r 55a53b5e308d -r 56bb29747b4d test-data/output_parsed_pairs_sam.pairs
--- a/test-data/output_parsed_pairs_sam.pairs Tue Apr 30 12:02:29 2024 +0000
+++ b/test-data/output_parsed_pairs_sam.pairs Tue May 21 16:03:55 2024 +0000

@@ -4,7 +4,7 @@
#chromsize: Test_seq 450060
#samheader: @SQ SN:Test_seq LN:450060
#samheader: @PG ID:bwa-mem2 PN:bwa-mem2 VN:2.2.1 CL:bwa-mem2 mem -5SP -T0 -t 8 test test_hic_reads_1.fq test_hic_reads_2.fq
-#samheader: @PG ID:pairtools_parse PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/2/e/1/dataset_2e1a2abe-d4ed-46d7-90b0-02f7ad21e679.dat -c /tmp/tmpchj83off/files/4/0/d/dataset_40dde3ed-dc87-49a5-b6d7-c9bb448a57ee.dat -o /tmp/tmpchj83off/job_working_directory/000/3/outputs/dataset_bb5fe9ed-7777-4b2b-88c3-9f89a9d6e0ce.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-mem2 VN:1.1.0
+#samheader: @PG ID:pairtools_parse PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/9/8/8/dataset_988a4d9d-9695-43af-830e-80c6375afe07.dat -c /tmp/tmprvti6kw7/files/1/e/2/dataset_1e224097-dd1a-40f1-bb9b-4234ec9f8cb7.dat -o /tmp/tmprvti6kw7/job_working_directory/000/3/outputs/dataset_bbc176bc-490b-4d30-b0e8-7f401863a12e.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-mem2 VN:1.1.0
#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2
A00126:224:H7HMWDSX3:3:1101:4779:3098 Test_seq 166211 Test_seq 214901 - - UU A00126:224:H7HMWDSX3:3:1101:4779:3098113Test_seq1661344378M=21482448691GGGCACCAACTAGTTCTTCTGGTCTCAGGATAATGTAGGTCTCTGGTTCATGTGGCCCTTTCTGTCTCTTGGGTTCTTFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFNM:i:0MD:Z:78MC:Z:78MAS:i:78XS:i:63XA:Z:Test_seq,+214829,5S73M,2;Yt:Z:UU A00126:224:H7HMWDSX3:3:1101:4779:3098177Test_seq214824578M=166134-48691AAGAGCCCAAGAGACAGAAAGGGCCACATGAACCACAGACCTACATCATCCTGAGACCAGAAGAACTAGTTGGTGCCCFFFF,FFFFFFFFFFFFF,FFFFFFFFFFFF:FF:,FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFNM:i:3MD:Z:1T33G33A8MC:Z:78MAS:i:66XS:i:63XA:Z:Test_seq,+166134,78M,3;Yt:Z:UU
A00126:224:H7HMWDSX3:3:1101:2908:3239 Test_seq 167331 Test_seq 167696 + - UU A00126:224:H7HMWDSX3:3:1101:2908:3239161Test_seq16733123151M=167546366TGAGATGTCATAGCTGAATATTCTTTCCCAGTCTGTAGGTGGTCTTTTTACTCTTTTGGTGAAGTCTTTAGATGAGCATAGGTGTTTGATTTTTAGGAGCTCCCAGTTATCTGGTTTCTCTTCATCATTTTTGGTAATGTTTTGTATTCTGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFF:FFFFF:FFFF:FFFFFFFFFFFFFFF:FF,,FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF:FFFFFFFF:FF,FFNM:i:1MD:Z:37A113MC:Z:151MAS:i:146XS:i:135XA:Z:Test_seq,-213553,151M,4;Yt:Z:UU A00126:224:H7HMWDSX3:3:1101:2908:323981Test_seq16754644151M=167331-366TAGTCTTTATGTTTAGGTCTTTGATCCACTTGGAGTTAGTTTTTGTGCATGGTGTGAGGTATGGGTCCTGTTTCATTCTTTTACAAATGGATATCCAGGTATGCCAGCACCATTTGTTAAAAAGACTATTATTTCCCCAATTGACTGACACFF,F,F:FFFFFFFFF,FFF:FFFFFF:FFFF:FFFFFFFFFFF:FF::F,FFFFFFFFF:,F,FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FFF::FFFFFFFFFFFFF,FFFFFFF:FF:F,:FFFFFFFFFF,F,F:FFFFFFFFFFNM:i:3MD:Z:82G15T30C21MC:Z:151MAS:i:136XS:i:114XA:Z:Test_seq,+213342,118M2I23M2I6M,8;Yt:Z:UU

diff -r 55a53b5e308d -r 56bb29747b4d test-data/output_parsed_pairs_sam_assemblyname.pairs
--- a/test-data/output_parsed_pairs_sam_assemblyname.pairs Tue Apr 30 12:02:29 2024 +0000
+++ b/test-data/output_parsed_pairs_sam_assemblyname.pairs Tue May 21 16:03:55 2024 +0000

@@ -4,7 +4,7 @@
#chromsize: Test_seq 450060
#samheader: @SQ SN:Test_seq LN:450060
#samheader: @PG ID:bwa-mem2 PN:bwa-mem2 VN:2.2.1 CL:bwa-mem2 mem -5SP -T0 -t 8 test test_hic_reads_1.fq test_hic_reads_2.fq
-#samheader: @PG ID:pairtools_parse PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/5/2/e/dataset_52effa56-a42c-41a9-802e-401d7a5813de.dat -c /tmp/tmpchj83off/files/8/d/d/dataset_8dd0a91e-ecbd-4f98-86cd-2510709cac82.dat --assembly test_assembly -o /tmp/tmpchj83off/job_working_directory/000/28/outputs/dataset_0a87c13d-5811-4e81-9626-bb8665d07df4.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-mem2 VN:1.1.0
+#samheader: @PG ID:pairtools_parse PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/6/0/0/dataset_600103a3-0dfd-425e-9758-fd74483e7fba.dat -c /tmp/tmprvti6kw7/files/9/4/6/dataset_946e6de4-4d3a-422e-a73b-b8f7646b510d.dat --assembly test_assembly -o /tmp/tmprvti6kw7/job_working_directory/000/28/outputs/dataset_65c0af76-60c7-4aac-b926-a405b8e6f3cf.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-mem2 VN:1.1.0
#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2
A00126:224:H7HMWDSX3:3:1101:4779:3098 Test_seq 166211 Test_seq 214901 - - UU A00126:224:H7HMWDSX3:3:1101:4779:3098113Test_seq1661344378M=21482448691GGGCACCAACTAGTTCTTCTGGTCTCAGGATAATGTAGGTCTCTGGTTCATGTGGCCCTTTCTGTCTCTTGGGTTCTTFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFNM:i:0MD:Z:78MC:Z:78MAS:i:78XS:i:63XA:Z:Test_seq,+214829,5S73M,2;Yt:Z:UU A00126:224:H7HMWDSX3:3:1101:4779:3098177Test_seq214824578M=166134-48691AAGAGCCCAAGAGACAGAAAGGGCCACATGAACCACAGACCTACATCATCCTGAGACCAGAAGAACTAGTTGGTGCCCFFFF,FFFFFFFFFFFFF,FFFFFFFFFFFF:FF:,FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFNM:i:3MD:Z:1T33G33A8MC:Z:78MAS:i:66XS:i:63XA:Z:Test_seq,+166134,78M,3;Yt:Z:UU
A00126:224:H7HMWDSX3:3:1101:2908:3239 Test_seq 167331 Test_seq 167696 + - UU A00126:224:H7HMWDSX3:3:1101:2908:3239161Test_seq16733123151M=167546366TGAGATGTCATAGCTGAATATTCTTTCCCAGTCTGTAGGTGGTCTTTTTACTCTTTTGGTGAAGTCTTTAGATGAGCATAGGTGTTTGATTTTTAGGAGCTCCCAGTTATCTGGTTTCTCTTCATCATTTTTGGTAATGTTTTGTATTCTGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFF:FFFFF:FFFF:FFFFFFFFFFFFFFF:FF,,FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF:FFFFFFFF:FF,FFNM:i:1MD:Z:37A113MC:Z:151MAS:i:146XS:i:135XA:Z:Test_seq,-213553,151M,4;Yt:Z:UU A00126:224:H7HMWDSX3:3:1101:2908:323981Test_seq16754644151M=167331-366TAGTCTTTATGTTTAGGTCTTTGATCCACTTGGAGTTAGTTTTTGTGCATGGTGTGAGGTATGGGTCCTGTTTCATTCTTTTACAAATGGATATCCAGGTATGCCAGCACCATTTGTTAAAAAGACTATTATTTCCCCAATTGACTGACACFF,F,F:FFFFFFFFF,FFF:FFFFFF:FFFF:FFFFFFFFFFF:FF::F,FFFFFFFFF:,F,FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FFF::FFFFFFFFFFFFF,FFFFFFF:FF:F,:FFFFFFFFFF,F,F:FFFFFFFFFFNM:i:3MD:Z:82G15T30C21MC:Z:151MAS:i:136XS:i:114XA:Z:Test_seq,+213342,118M2I23M2I6M,8;Yt:Z:UU

diff -r 55a53b5e308d -r 56bb29747b4d test-data/output_sorted_pairs.pairs
--- a/test-data/output_sorted_pairs.pairs Tue Apr 30 12:02:29 2024 +0000
+++ b/test-data/output_sorted_pairs.pairs Tue May 21 16:03:55 2024 +0000

b'@@ -19,7 +19,7 @@\n #chromsize: chrXV 1091291\n #chromsize: chrXVI 948066\n #chromsize: chrM 85779\n-#samheader: @HD\tVN:1.6\tSO:coordinate\n+#samheader: @HD\tVN:1.6\tSO:queryname\n #samheader: @SQ\tSN:chrI\tLN:230218\n #samheader: @SQ\tSN:chrII\tLN:813184\n #samheader: @SQ\tSN:chrIII\tLN:316620\n@@ -38,711 +38,738 @@\n #samheader: @SQ\tSN:chrXV\tLN:1091291\n #samheader: @SQ\tSN:chrXVI\tLN:948066\n #samheader: @PG\tID:bwa\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/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\tPP:bwa\tVN:1.1.0\n-#samheader: @PG\tID:pairtools_sort-1.3\tPN:pairtools_sort\tCL:/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\tPP:pairtools_parse-1.2\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-1.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/3/a/6/dataset_3a6251e3-16fc-4685-babe-d12b42999e62.dat -c /tmp/tmprvti6kw7/files/5/6/2/dataset_562f805b-59bf-489a-8b58-f6e996bc1d69.dat -o /tmp/tmprvti6kw7/job_working_directory/000/7/outputs/dataset_3f99deff-4f79-499c-b1a1-93c99ce1de58.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-1.3\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpcoq066hp/files/4/c/9/dataset_4c944e13-b355-4fa3-8cb8-ade0c8a0304f.dat -o /tmp/tmpcoq066hp/job_working_directory/000/2/outputs/dataset_f402d591-2bd8-446d-939a-51334f085147.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-1.2\tVN:1.1.0\n #samheader: @PG\tID:bwa-2CCE5976\tPN:bwa\tVN:0.7.15-r1140\tCL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz\n-#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/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\tPP:bwa-2CCE5976\tVN:1.1.0\n-#samheader: @PG\tID:pairtools_sort-2.3\tPN:pairtools_sort\tCL:/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\tPP:pairtools_parse-2.2\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_parse-2.2\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmprvti6kw7/files/3/a/6/dataset_3a6251e3-16fc-4685-babe-d12b42999e62.dat -c /tmp/tmprvti6kw7/files/5/6/2/dataset_562f805b-59bf-489a-8b58-f6e996bc1d69.dat -o /tmp/tmprvti6kw7/job_working_directory/000/7/outputs/dataset_3f99deff-4f79-499c-b1a1-93c99ce1de58.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-2CCE5976\tVN:1.1.0\n+#samheader: @PG\tID:pairtools_sort-2.3\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpcoq066hp/files/4/c/9/dataset_4c944e13-b355-4fa3-8cb8-ade0c8a0304f.dat -o /tmp/tmpcoq066hp/job_working_directory/000/2/outputs/dataset_f402d591-2bd8-446d-939a-51334f085147.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-2.2\tVN:1.1.0\n #samheader: @PG\tID:bwa-3CAFD9D9\tPN:bwa\tV'..b":1:1508:20322\x19177\x19chrXVI\x19721549\x1960\x1936M\x19=\x19714397\x19-7153\x19TATTAGCACATTTCCAGATAAAATTTCGATGACATN\x19@@@@@@@@@@@@@@@@22@@@@@@@@22313/---&\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:2251:19688\tchrXVI\t716030\tchrXVI\t716273\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:2251:19688\x1997\x19chrXVI\x19716030\x1960\x1936M\x19=\x19716238\x19244\x19AAGAATAGAAATGTAAATAATGAGTTAAAAGGGGCA\x19?+,*+58777@@@@@@@@@22@@@@@@@@@@@@@@@\x19NM:i:0\x19MD:Z:36\x19AS:i:36\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:2251:19688\x19145\x19chrXVI\x19716238\x1960\x1936M\x19=\x19716030\x19-244\x19TTAACAAAAGCTTGAGAGCTTTCAAGTTTTGAAGCN\x19@222@@CC@@@@CCC@C@@C@CCCCC888884444)\x19NM:i:1\x19MD:Z:35T0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:2051:4191\tchrXVI\t716323\tchrXVI\t751869\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:2051:4191\x19177\x19chrXVI\x19716288\x1958\x1936M\x19=\x19751834\x1935547\x19ACCATTTTTAAGCGAATTCTGAGAATCATTTGAGGN\x19####################################\x19NM:i:2\x19MD:Z:9G25A0\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:2051:4191\x19113\x19chrXVI\x19751834\x1960\x1936M\x19=\x19716288\x19-35547\x19TTTTGACGTAATCTTTTTGTAAAATGCTCCCTGAGT\x19####################################\x19NM:i:1\x19MD:Z:35A0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n HWUSI-EAS1533_0033_FC:1:1:1430:3252\tchrXVI\t717154\tchrXVI\t718860\t-\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:1430:3252\x19113\x19chrXVI\x19717119\x1960\x1936M\x19=\x19718825\x191707\x19CATTATAGGTTCGGTGCGAAAAGCATACCAAATTCG\x19####################################\x19NM:i:1\x19MD:Z:35T0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:1430:3252\x19177\x19chrXVI\x19718825\x1960\x1936M\x19=\x19717119\x19-1707\x19TCTTTTATCATCCAAATCAACTGATAAGGAATAAAN\x1922237::7::7@@@@@:<<<<33313(*'&''&0(%\x19NM:i:1\x19MD:Z:35T0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n HWUSI-EAS1533_0033_FC:1:1:1270:7373\tchrXVI\t730548\tchrXVI\t730761\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:1270:7373\x19161\x19chrXVI\x19730548\x1960\x1936M\x19=\x19730726\x19214\x19NATTGATCAATTAGTAAAGAAGGAATTTGCGAATAT\x19%(((*+**+-7777/9989722@1@@@@@@<5<<<@\x19NM:i:2\x19MD:Z:0A2A32\x19AS:i:32\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:1270:7373\x1981\x19chrXVI\x19730726\x1960\x1936M\x19=\x19730548\x19-214\x19TTTAATGACGACGATGATACTTTATTTTTGGAAGAT\x19####################################\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n HWI-ST560:29:B0A7LABXX:2:1101:18943:15526\tchrXVI\t752962\tchrXVI\t753241\t+\t-\tUU\tHWI-ST560:29:B0A7LABXX:2:1101:18943:15526\x1997\x19chrXVI\x19752962\x1960\x1950M\x19=\x19753192\x19280\x19ATATTTTATTTATGTGTAGTTTTTATTTATGTGAAATGGAACATTCTTTG\x1911144422,22222AE:?FFEAEDD>EA4A@EF4AEE>C9*:?*9C####\x19NM:i:2\x19MD:Z:2C43G3\x19AS:i:43\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:18943:15526\x19145\x19chrXVI\x19753192\x1944\x1950M\x19=\x19752962\x19-280\x19TTGGACAGATCTAACAGAAAAATAAGAAGACCTCTCCTCTATCTCAAGCT\x19??:*:?*?1*1**1*9@*:*>FAFA+4AE@D@?BEGDBC<2+BDDFFB??\x19NM:i:3\x19MD:Z:11A2A7G27\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n HWI-ST560:29:B0A7LABXX:2:1101:16774:5417\tchrXVI\t813494\tchrXVI\t813775\t+\t-\tUU\tHWI-ST560:29:B0A7LABXX:2:1101:16774:5417\x19161\x19chrXVI\x19813494\x1960\x1950M\x19=\x19813726\x19282\x19GTTTTTTCCCGGTTATACTAAACGGTAAGACGCTTTTACCATTACATGAG\x19B=@DDDFFHHHG<CGFGAEEGIJIIHGGGGIIIBGHGIIHGIIEHGGHIJ\x19NM:i:0\x19MD:Z:50\x19AS:i:50\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:16774:5417\x1981\x19chrXVI\x19813726\x1960\x1950M\x19=\x19813494\x19-282\x19CACCACTGAAAAAGCATCTAAAGGTGAGGTACAATTGCAAATATAAAGCT\x19BBGFCIIIIGFF?:HHGIIIJIIIJJIJJIAFGHFA<<24242224+111\x19NM:i:0\x19MD:Z:50\x19AS:i:50\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:1716:21250\tchrXVI\t862498\tchrXVI\t873542\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:1716:21250\x19161\x19chrXVI\x19862498\x1958\x1936M\x19=\x19873507\x1911045\x19NTGAATTACAGAGAGTTTTGATCGATCTAGAAAAAC\x19&/---77777@@@@@@@@@@38888@@@@@@@@222\x19NM:i:2\x19MD:Z:0T19G15\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:1716:21250\x1981\x19chrXVI\x19873507\x1960\x1936M\x19=\x19862498\x19-11045\x19CCTAACATCAAATAATGGAAATTTCTTATTAAAATG\x19CC@@CCCC22CC@CC@CCCC22@CCC888883232C\x19NM:i:1\x19MD:Z:35C0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n HWI-ST560:29:B0A7LABXX:2:1101:19165:17229\tchrXVI\t896753\tchrXVI\t897069\t+\t-\tUU\tHWI-ST560:29:B0A7LABXX:2:1101:19165:17229\x1997\x19chrXVI\x19896753\x1960\x1950M\x19=\x19897020\x19317\x19AGGTTTGAACAAATGAAAAGAGATGCGGCCGTATGGTGGGAAAATCTGGG\x1911++42222222+2A<>ECECE:3ACEAED<8??BD88(-8B=AA#####\x19NM:i:2\x19MD:Z:2C35T11\x19AS:i:42\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:19165:17229\x19145\x19chrXVI\x19897020\x1960\x1950M\x19=\x19896753\x19-317\x19CTATACTGTAGTTTCAGCCAAAAAAAATAATAAAAAAAGCATAATTGGAG\x19####DIGHD@FC==-)='.0>BE9FFEECBGIHGE<C?HF8FD?EDB<?@\x19NM:i:0\x19MD:Z:50\x19AS:i:50\x19XS:i:19\x19Yt:Z:UU\n"