| Next changeset 1:ccc7a8e707fb (2024-04-05) |
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Commit message:
planemo upload for repository https://github.com/open2c/pairtools commit e9ebcf7ac032fafaa445e654b245df679a4bbf18 |
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added:
dedup.xml macros.xml test-data/output_dedup_pairs.pairsam test-data/output_dedup_pairs.stats test-data/output_dedup_pairs_markdups.pairsam test-data/output_dedup_sorted.pairsam test-data/output_dups_pairs_markdups.pairsam test-data/output_parsed_pairs.stats 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_sorted_pairs.pairs test-data/output_sorted_pairs.pairsam test-data/test.bam test-data/test.genome test-data/test.reduced.chrom.sizes test-data/test.sam |
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| diff -r 000000000000 -r f8c1d2a93d43 dedup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dedup.xml Thu Apr 04 19:40:59 2024 +0000 |
| [ |
| @@ -0,0 +1,67 @@ +<tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT"> + <description>Find and remove PCR/optical duplicates</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + pairtools dedup + '$pairs_path' + -o '$output_dedup_pairs' + #if $output_dups: + --output-dups '$output_dups_pairs' + #end if + $mark_dups + #if $output_stats: + --output-stats '$dedup_pairs_stats' + #end if + --nproc-in \${GALAXY_SLOTS:-4} + --nproc-out \${GALAXY_SLOTS:-4} + ]]></command> + <inputs> + <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/> + <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="False" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/> + <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/> + <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/> + </inputs> + <outputs> + <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/> + <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs"> + <filter>output_dups</filter> + </data> + <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats"> + <filter>output_stats</filter> + </data> + </outputs> + <tests> + <!--Test 01 with default parameters--> + <test expect_num_outputs="1"> + <param name="pairs_path" value="output_sorted_pairs.pairsam"/> + <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" lines_diff="20"/> + </test> + <!--Test 02 mark_dups enabled and output_dups--> + <test expect_num_outputs="2"> + <param name="pairs_path" value="output_sorted_pairs.pairsam"/> + <param name="mark_dups" value="true"></param> + <param name="output_dups" value="true"></param> + <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/> + <output name="output_dups_pairs" file="output_dups_pairs_markdups.pairsam" lines_diff="20"/> + </test> + <!--Test 03 mark_dups and output_stats enabled--> + <test expect_num_outputs="2"> + <param name="pairs_path" value="output_sorted_pairs.pairsam"/> + <param name="mark_dups" value="true"></param> + <param name="output_stats" value="true"></param> + <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/> + <output name="dedup_pairs_stats" file="output_dedup_pairs.stats" lines_diff="20"/> + </test> + </tests> + <help><![CDATA[ + **Pairtools dedup** + + Find PCR/optical duplicates in an upper-triangular flipped sorted pairs/pairsam file. Allow for a +/-N bp mismatch at each side of duplicated molecules. + + ]]></help> + <expand macro="citations"/> + <expand macro="creator"/> +</tool> |
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| diff -r 000000000000 -r f8c1d2a93d43 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Apr 04 19:40:59 2024 +0000 |
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| @@ -0,0 +1,32 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.3</token> + <token name="@SUFFIX_VERSION@">0</token> + <xml name="edam_ontology"> + <edam_datas> + <edam_data>topic_1381</edam_data> + </edam_datas> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pairtools</requirement> + </requirements> + </xml> + <xml name="creator"> + <creator> + <organization name="IZW" url="https://www.izw-berlin.de/en/home.html"/> + </creator> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/2023.02.13.528389</citation> + </citations> + </xml> + <xml name="walks_policy_options"> + <option value="mask">mask - Mask walks (chrom="!", pos=0, strand="-")</option> + <option value="5any">5any - Report the 5'-most alignment on each side</option> + <option value="5unique" selected="true">5unique - Report the 5'-most unique alignment on each side, if present</option> + <option value="3any">3any - Report the 3'-most alignment on each side</option> + <option value="3unique">3unique - Report the 3'-most unique alignment on each side, if present</option> + <option value="all">all - Report all available unique alignments on each side</option> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_dedup_pairs.pairsam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dedup_pairs.pairsam Thu Apr 04 19:40:59 2024 +0000 |
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| b'@@ -0,0 +1,838 @@\n+## pairs format v1.0.0\n+#sorted: chr1-chr2-pos1-pos2\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\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:/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:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam\tPP:pairtools_sort-1.3\tVN:1.0.2\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:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam\tPP:pairtools_sort-2.3\tVN:1.0.2\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.reduced.chrom.sizes test.bam\tPP:bwa-3CAFD9D9\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_sort-3.3\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-3.2\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_dedup-3.4\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam\tPP:pairtools_sort-3.3\tVN:1'..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" |
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| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_dedup_pairs.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dedup_pairs.stats Thu Apr 04 19:40:59 2024 +0000 |
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| @@ -0,0 +1,275 @@ +total 1992 +total_unmapped 914 +total_single_sided_mapped 287 +total_mapped 791 +total_dups 9 +total_nodups 782 +cis 597 +trans 185 +pair_types/NN 853 +pair_types/UU 782 +pair_types/NU 234 +pair_types/MU 53 +pair_types/MM 40 +pair_types/NM 21 +pair_types/DD 9 +cis_1kb+ 185 +cis_2kb+ 171 +cis_4kb+ 151 +cis_10kb+ 114 +cis_20kb+ 80 +cis_40kb+ 46 +summary/frac_cis 0.7634271099744245 +summary/frac_cis_1kb+ 0.23657289002557544 +summary/frac_cis_2kb+ 0.2186700767263427 +summary/frac_cis_4kb+ 0.19309462915601022 +summary/frac_cis_10kb+ 0.14578005115089515 +summary/frac_cis_20kb+ 0.10230179028132992 +summary/frac_cis_40kb+ 0.058823529411764705 +summary/frac_dups 0.011378002528445006 +summary/complexity_naive 34495.88583157276 +chrom_freq/chrIV/chrIV 83 +chrom_freq/chrVII/chrVII 55 +chrom_freq/chrXV/chrXV 53 +chrom_freq/chrXIII/chrXIII 46 +chrom_freq/chrII/chrII 41 +chrom_freq/chrXVI/chrXVI 40 +chrom_freq/chrXIV/chrXIV 37 +chrom_freq/chrX/chrX 37 +chrom_freq/chrXII/chrXII 36 +chrom_freq/chrXI/chrXI 36 +chrom_freq/chrM/chrM 33 +chrom_freq/chrVIII/chrVIII 30 +chrom_freq/chrIX/chrIX 22 +chrom_freq/chrV/chrV 21 +chrom_freq/chrIII/chrIII 12 +chrom_freq/chrVI/chrVI 8 +chrom_freq/chrI/chrI 7 +chrom_freq/chrVII/chrXV 6 +chrom_freq/chrIV/chrXII 6 +chrom_freq/chrIV/chrXIII 6 +chrom_freq/chrVII/chrXII 6 +chrom_freq/chrII/chrVII 5 +chrom_freq/chrXII/chrXIII 5 +chrom_freq/chrIV/chrX 5 +chrom_freq/chrX/chrXIV 4 +chrom_freq/chrII/chrIV 4 +chrom_freq/chrII/chrXVI 4 +chrom_freq/chrXIV/chrXVI 4 +chrom_freq/chrII/chrXIV 4 +chrom_freq/chrVII/chrXIV 4 +chrom_freq/chrXI/chrXV 4 +chrom_freq/chrXI/chrXII 4 +chrom_freq/chrIV/chrVII 4 +chrom_freq/chrXIII/chrXV 3 +chrom_freq/chrXI/chrXVI 3 +chrom_freq/chrII/chrXIII 3 +chrom_freq/chrXI/chrXIII 3 +chrom_freq/chrVII/chrIX 3 +chrom_freq/chrVIII/chrXIII 3 +chrom_freq/chrX/chrXII 3 +chrom_freq/chrX/chrXIII 3 +chrom_freq/chrXIII/chrXIV 3 +chrom_freq/chrV/chrXVI 3 +chrom_freq/chrIV/chrV 3 +chrom_freq/chrIV/chrVIII 3 +chrom_freq/chrIV/chrXI 3 +chrom_freq/chrIV/chrXV 3 +chrom_freq/chrIV/chrXVI 3 +chrom_freq/chrXV/chrXVI 3 +chrom_freq/chrIX/chrXII 3 +chrom_freq/chrXIII/chrXVI 2 +chrom_freq/chrX/chrXVI 2 +chrom_freq/chrIV/chrVI 2 +chrom_freq/chrIV/chrXIV 2 +chrom_freq/chrXI/chrXIV 2 +chrom_freq/chrVII/chrXVI 2 +chrom_freq/chrIX/chrX 2 +chrom_freq/chrVII/chrVIII 2 +chrom_freq/chrIII/chrX 2 +chrom_freq/chrIX/chrXV 2 +chrom_freq/chrIII/chrV 2 +chrom_freq/chrXIV/chrXV 2 +chrom_freq/chrXII/chrXV 2 +chrom_freq/chrV/chrX 2 +chrom_freq/chrI/chrX 2 +chrom_freq/chrII/chrXV 2 +chrom_freq/chrII/chrVIII 1 +chrom_freq/chrXII/chrXIV 1 +chrom_freq/chrXII/chrXVI 1 +chrom_freq/chrII/chrX 1 +chrom_freq/chrI/chrXV 1 +chrom_freq/chrIII/chrXIII 1 +chrom_freq/chrII/chrXI 1 +chrom_freq/chrVI/chrX 1 +chrom_freq/chrIII/chrVIII 1 +chrom_freq/chrIX/chrXI 1 +chrom_freq/chrV/chrM 1 +chrom_freq/chrV/chrVI 1 +chrom_freq/chrV/chrXI 1 +chrom_freq/chrV/chrXIII 1 +chrom_freq/chrV/chrXIV 1 +chrom_freq/chrV/chrXV 1 +chrom_freq/chrVI/chrXI 1 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| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_dedup_pairs_markdups.pairsam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dedup_pairs_markdups.pairsam Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,838 @@\n+## pairs format v1.0.0\n+#sorted: chr1-chr2-pos1-pos2\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\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:/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:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-1.3\tVN:1.0.2\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:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-2.3\tVN:1.0.2\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.reduced.chrom.sizes test.bam\tPP:bwa-3CAFD9D9\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_sort-3.3\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-3.2\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_dedup-3.4\tPN:pairtools_dedup\tCL:/scratch/ddepanis/Software/anaco'..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" |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_dedup_sorted.pairsam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dedup_sorted.pairsam Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,842 @@\n+## pairs format v1.0.0\n+#sorted: chr1-chr2-pos1-pos2\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\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:/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:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-1.3\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_sort-1.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/c/1/c/dataset_c1c8eade-049e-4209-b8f9-a97c31df8468.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/4/outputs/dataset_22fb7731-5e54-4b91-9180-5373e3456c9c.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-1.4\tVN:1.0.3\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:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam\tPP:pairtools_sort-2.3\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_sort-2.5\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/c/1/c/dataset_c1c8eade-049e-4209-b8f9-a97c31df8468.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/4/outputs/dataset_22fb7731-5e54-4b91-9180-5373e3456c9c.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_dedup-2.4\tVN:1.0.3\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.fa'..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" |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_dups_pairs_markdups.pairsam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_dups_pairs_markdups.pairsam Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,65 @@\n+## pairs format v1.0.0\n+#sorted: chr1-chr2-pos1-pos2\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\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:/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:/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\tPP:pairtools_sort-1.3\tVN:1.0.2\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:/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\tPP:pairtools_sort-2.3\tVN:1.0.2\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.reduced.chrom.sizes test.bam\tPP:bwa-3CAFD9D9\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_sort-3.3\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-3.2\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_dedup-3.4\tPN:pairtools_dedup\tCL:/scratch/ddepan'..b':Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:2403:20808\tchrIV\t497939\tchrIV\t498215\t+\t-\tDD\tHWUSI-EAS1533_0033_FC:1:1:2403:20808\x1997\x19chrIV\x19497939\x1960\x1936M\x19=\x19498180\x19277\x19CGCTTTCATTACTCGAATCCGTCAAAGACGCTTCTT\x194544588888C@@CC@CCC@@@C@@@C@CCC@C@CC\x19NM:i:1\x19MD:Z:0A35\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:2403:20808\x19145\x19chrIV\x19498180\x1960\x1936M\x19=\x19497939\x19-277\x19GGCTGGTGAAGGAGTATTATTTACAATTCTAAAGCN\x19@@C@@@@CC@CC@CC22C@@@CCCCC888886666)\x19NM:i:1\x19MD:Z:35T0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWI-ST560:29:B0A7LABXX:2:1101:20583:3832\tchrIV\t623680\tchrIV\t623930\t+\t-\tDD\tHWI-ST560:29:B0A7LABXX:2:1101:20583:3832\x19161\x19chrIV\x19623680\x1960\x1950M\x19=\x19623881\x19251\x19TAAACAGTTAATGAAATCAGTTGTTACAAATGAGTTTCAATGCAGCTTAA\x19BBCFDFDDHHFCHGIII<ABHHHHIHFHFDGIIIIJJJJJGIIDHICGGG\x19NM:i:0\x19MD:Z:50\x19AS:i:50\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:20583:3832\x1981\x19chrIV\x19623881\x1944\x1950M\x19=\x19623680\x19-251\x19GGATCATCTAGATGAAGAGTTGGACCTGACTGGGCCGATAAACAACTCAC\x19B909DHD?F?*?*GHFF???:*11IHHFAFFGFGC<23233322244141\x19NM:i:3\x19MD:Z:5G6G8T28\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWI-ST560:29:B0A7LABXX:2:1101:21049:12870\tchrVII\t395112\tchrVII\t395330\t+\t-\tDD\tHWI-ST560:29:B0A7LABXX:2:1101:21049:12870\x1997\x19chrVII\x19395112\x1960\x193S47M\x19=\x19395298\x19219\x19AAATTTTATCATAAAGATGAAAAACCTCGACCACGTTTTGCACATCAGCA\x19##################################################\x19NM:i:3\x19MD:Z:9C9C4T22\x19AS:i:32\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:21049:12870\x19145\x19chrVII\x19395298\x1960\x1917S33M\x19=\x19395112\x19-219\x19TCGAAGGTAGACATCTTACTTGTAGTACCACAACTGAATGAAATCTTGCT\x19####################EHDC4A3EA<3<,,9<?4C2:+3A8DD@<=\x19NM:i:0\x19MD:Z:33\x19AS:i:33\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:2739:11140\tchrVIII\t403630\tchrVIII\t403904\t+\t-\tDD\tHWUSI-EAS1533_0033_FC:1:1:2739:11140\x19161\x19chrVIII\x19403630\x1958\x1936M\x19=\x19403869\x19275\x19NGCTTGCTACTTTGTGCGAGCTTGATATGCAGGACA\x19(22/277777C@CCCCC@@CCC@@C@@@CC@@@@@C\x19NM:i:2\x19MD:Z:0A15T19\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:2739:11140\x1981\x19chrVIII\x19403869\x1960\x1936M\x19=\x19403630\x19-275\x19AGTTTTTCTGACGATCTGAAGTCTGTTTACCAAGCA\x19@444CCCC@@CC@@@CC@CCCCCCCC877773333=\x19NM:i:1\x19MD:Z:35T0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWI-ST560:29:B0A7LABXX:2:1101:20782:17358\tchrXIII\t538121\tchrXIII\t544653\t-\t-\tDD\tHWI-ST560:29:B0A7LABXX:2:1101:20782:17358\x19177\x19chrXIII\x19538072\x1960\x1950M\x19=\x19544604\x196533\x19GAGCTTCATCGGATGTTGGTGAGTGATGAATATCACGGTAAAGAATACAA\x193HEGED86)6GGHCHGDC2A<AEHA<<AHGHHDC1HHDHD?FAFDB=@@B\x19NM:i:1\x19MD:Z:0A49\x19AS:i:49\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:20782:17358\x19113\x19chrXIII\x19544604\x1960\x1950M\x19=\x19538072\x19-6533\x19TATTGCGCTGACTTCGTTATCATTCAAGCTAACTAGTTCTTCCTCGTCTG\x19AFGAGEGHF?0=HGFDB<CC4:1)FIIHGFF<C<2222230000044111\x19NM:i:1\x19MD:Z:23G26\x19AS:i:45\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:1306:18143\tchrXIII\t794677\tchrXIII\t794956\t+\t-\tDD\tHWUSI-EAS1533_0033_FC:1:1:1306:18143\x19161\x19chrXIII\x19794677\x1960\x1936M\x19=\x19794921\x19280\x19NAGGTGGCAGCATAGCACTGTAATGAGATATATTAA\x19%&(&)*)*+,:1:::<<<:0::3::@@@5@@@:@@@\x19NM:i:1\x19MD:Z:0G35\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:1306:18143\x1981\x19chrXIII\x19794921\x1960\x1936M\x19=\x19794677\x19-280\x19GGCTAGGCCAGTTAATACAAACGCTGAAACGGAATG\x19####################################\x19NM:i:1\x19MD:Z:35C0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWI-ST560:29:B0A7LABXX:2:1101:19177:20440\tchrXV\t1012747\tchrXV\t1012994\t+\t-\tDD\tHWI-ST560:29:B0A7LABXX:2:1101:19177:20440\x1997\x19chrXV\x191012747\x1960\x1950M\x19=\x191012945\x19248\x19GATCTGCTTATTAAATCTGGCATAATAAAGTTGATTGTCTTGACGTTGCA\x1911+44224222222<C<AEI:CBEIGIBH><FCHIBFHGHIGIII8?FFH\x19NM:i:0\x19MD:Z:50\x19AS:i:50\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:19177:20440\x19145\x19chrXV\x191012945\x1960\x1950M\x19=\x191012747\x19-248\x19AACTTTTAACTCGGGAAATATGTATCACTATACTAAAAAACATTAATTTA\x19BFIGGGIIGGG@CBCFBCHHIHHH@FF<DF<FFE?DAHFCFA+?DBD@@?\x19NM:i:0\x19MD:Z:50\x19AS:i:50\x19XS:i:0\x19Yt:Z:UU\n+HWI-ST560:29:B0A7LABXX:2:1101:15890:13657\tchrXVI\t416774\tchrXVI\t486947\t-\t-\tDD\tHWI-ST560:29:B0A7LABXX:2:1101:15890:13657\x19113\x19chrXVI\x19416725\x1951\x1950M\x19=\x19486898\x1970174\x19AGGGAGTAACAACGGATCGCAGTCAAATGAACTTCAGATACGGTATAAGC\x19#######?9?93???@/@?<>)<@>=>89933).@?=22202))222000\x19NM:i:3\x19MD:Z:2T18T20T7\x19AS:i:37\x19XS:i:0\x19Yt:Z:UU\tHWI-ST560:29:B0A7LABXX:2:1101:15890:13657\x19177\x19chrXVI\x19486898\x1948\x1950M\x19=\x19416725\x19-70174\x19GAGAAACTTTTCATCAAAGCTAAAAGGCACTCACACAAGCCTTCCCGTCC\x19B8BD>BF?*D>D?<GCG?*)@@IGBC*?1C1C2FAAGDDF<))DDA+=B=\x19NM:i:3\x19MD:Z:19A6T19T3\x19AS:i:36\x19XS:i:0\x19Yt:Z:UU\n' |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_parsed_pairs.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_parsed_pairs.stats Thu Apr 04 19:40:59 2024 +0000 |
| b |
| @@ -0,0 +1,186 @@ +total 592 +total_unmapped 53 +total_single_sided_mapped 231 +total_mapped 308 +total_dups 0 +total_nodups 308 +cis 308 +trans 0 +pair_types/MU 88 +pair_types/UU 293 +pair_types/MM 49 +pair_types/UR 8 +pair_types/MR 26 +pair_types/NR 110 +pair_types/RU 7 +pair_types/nM 3 +pair_types/Mu 7 +pair_types/NM 1 +cis_1kb+ 15 +cis_2kb+ 14 +cis_4kb+ 14 +cis_10kb+ 12 +cis_20kb+ 9 +cis_40kb+ 9 +summary/frac_cis 1.0 +summary/frac_cis_1kb+ 0.048701298701298704 +summary/frac_cis_2kb+ 0.045454545454545456 +summary/frac_cis_4kb+ 0.045454545454545456 +summary/frac_cis_10kb+ 0.03896103896103896 +summary/frac_cis_20kb+ 0.02922077922077922 +summary/frac_cis_40kb+ 0.02922077922077922 +summary/frac_dups 0.0 +summary/complexity_naive nan +chrom_freq/Test_seq/Test_seq 308 +dist_freq/0-1/+- 0 +dist_freq/0-1/-+ 0 +dist_freq/0-1/-- 0 +dist_freq/0-1/++ 0 +dist_freq/1-2/+- 0 +dist_freq/1-2/-+ 0 +dist_freq/1-2/-- 0 +dist_freq/1-2/++ 0 +dist_freq/2-3/+- 0 +dist_freq/2-3/-+ 0 +dist_freq/2-3/-- 0 +dist_freq/2-3/++ 0 +dist_freq/3-6/+- 0 +dist_freq/3-6/-+ 0 +dist_freq/3-6/-- 0 +dist_freq/3-6/++ 0 +dist_freq/6-10/+- 0 +dist_freq/6-10/-+ 0 +dist_freq/6-10/-- 0 +dist_freq/6-10/++ 0 +dist_freq/10-18/+- 0 +dist_freq/10-18/-+ 0 +dist_freq/10-18/-- 0 +dist_freq/10-18/++ 0 +dist_freq/18-32/+- 0 +dist_freq/18-32/-+ 0 +dist_freq/18-32/-- 0 +dist_freq/18-32/++ 0 +dist_freq/32-56/+- 0 +dist_freq/32-56/-+ 0 +dist_freq/32-56/-- 0 +dist_freq/32-56/++ 0 +dist_freq/56-100/+- 1 +dist_freq/56-100/-+ 0 +dist_freq/56-100/-- 0 +dist_freq/56-100/++ 0 +dist_freq/100-178/+- 3 +dist_freq/100-178/-+ 0 +dist_freq/100-178/-- 0 +dist_freq/100-178/++ 0 +dist_freq/178-316/+- 53 +dist_freq/178-316/-+ 0 +dist_freq/178-316/-- 0 +dist_freq/178-316/++ 0 +dist_freq/316-562/+- 236 +dist_freq/316-562/-+ 0 +dist_freq/316-562/-- 0 +dist_freq/316-562/++ 0 +dist_freq/562-1000/+- 0 +dist_freq/562-1000/-+ 0 +dist_freq/562-1000/-- 0 +dist_freq/562-1000/++ 0 +dist_freq/1000-1778/+- 1 +dist_freq/1000-1778/-+ 0 +dist_freq/1000-1778/-- 0 +dist_freq/1000-1778/++ 0 +dist_freq/1778-3162/+- 0 +dist_freq/1778-3162/-+ 0 +dist_freq/1778-3162/-- 0 +dist_freq/1778-3162/++ 0 +dist_freq/3162-5623/+- 0 +dist_freq/3162-5623/-+ 0 +dist_freq/3162-5623/-- 0 +dist_freq/3162-5623/++ 0 +dist_freq/5623-10000/+- 2 +dist_freq/5623-10000/-+ 0 +dist_freq/5623-10000/-- 0 +dist_freq/5623-10000/++ 0 +dist_freq/10000-17783/+- 1 +dist_freq/10000-17783/-+ 1 +dist_freq/10000-17783/-- 0 +dist_freq/10000-17783/++ 0 +dist_freq/17783-31623/+- 1 +dist_freq/17783-31623/-+ 0 +dist_freq/17783-31623/-- 0 +dist_freq/17783-31623/++ 0 +dist_freq/31623-56234/+- 0 +dist_freq/31623-56234/-+ 0 +dist_freq/31623-56234/-- 0 +dist_freq/31623-56234/++ 1 +dist_freq/56234-100000/+- 2 +dist_freq/56234-100000/-+ 0 +dist_freq/56234-100000/-- 1 +dist_freq/56234-100000/++ 1 +dist_freq/100000-177828/+- 1 +dist_freq/100000-177828/-+ 0 +dist_freq/100000-177828/-- 1 +dist_freq/100000-177828/++ 2 +dist_freq/177828-316228/+- 0 +dist_freq/177828-316228/-+ 0 +dist_freq/177828-316228/-- 0 +dist_freq/177828-316228/++ 0 +dist_freq/316228-562341/+- 0 +dist_freq/316228-562341/-+ 0 +dist_freq/316228-562341/-- 0 +dist_freq/316228-562341/++ 0 +dist_freq/562341-1000000/+- 0 +dist_freq/562341-1000000/-+ 0 +dist_freq/562341-1000000/-- 0 +dist_freq/562341-1000000/++ 0 +dist_freq/1000000-1778279/+- 0 +dist_freq/1000000-1778279/-+ 0 +dist_freq/1000000-1778279/-- 0 +dist_freq/1000000-1778279/++ 0 +dist_freq/1778279-3162278/+- 0 +dist_freq/1778279-3162278/-+ 0 +dist_freq/1778279-3162278/-- 0 +dist_freq/1778279-3162278/++ 0 +dist_freq/3162278-5623413/+- 0 +dist_freq/3162278-5623413/-+ 0 +dist_freq/3162278-5623413/-- 0 +dist_freq/3162278-5623413/++ 0 +dist_freq/5623413-10000000/+- 0 +dist_freq/5623413-10000000/-+ 0 +dist_freq/5623413-10000000/-- 0 +dist_freq/5623413-10000000/++ 0 +dist_freq/10000000-17782794/+- 0 +dist_freq/10000000-17782794/-+ 0 +dist_freq/10000000-17782794/-- 0 +dist_freq/10000000-17782794/++ 0 +dist_freq/17782794-31622777/+- 0 +dist_freq/17782794-31622777/-+ 0 +dist_freq/17782794-31622777/-- 0 +dist_freq/17782794-31622777/++ 0 +dist_freq/31622777-56234133/+- 0 +dist_freq/31622777-56234133/-+ 0 +dist_freq/31622777-56234133/-- 0 +dist_freq/31622777-56234133/++ 0 +dist_freq/56234133-100000000/+- 0 +dist_freq/56234133-100000000/-+ 0 +dist_freq/56234133-100000000/-- 0 +dist_freq/56234133-100000000/++ 0 +dist_freq/100000000-177827941/+- 0 +dist_freq/100000000-177827941/-+ 0 +dist_freq/100000000-177827941/-- 0 +dist_freq/100000000-177827941/++ 0 +dist_freq/177827941-316227766/+- 0 +dist_freq/177827941-316227766/-+ 0 +dist_freq/177827941-316227766/-- 0 +dist_freq/177827941-316227766/++ 0 +dist_freq/316227766-562341325/+- 0 +dist_freq/316227766-562341325/-+ 0 +dist_freq/316227766-562341325/-- 0 +dist_freq/316227766-562341325/++ 0 +dist_freq/562341325-1000000000/+- 0 +dist_freq/562341325-1000000000/-+ 0 +dist_freq/562341325-1000000000/-- 0 +dist_freq/562341325-1000000000/++ 0 +dist_freq/562341325+/+- 0 +dist_freq/562341325+/-+ 0 +dist_freq/562341325+/-- 0 +dist_freq/562341325+/++ 0 |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_parsed_pairs_bam.pairs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_parsed_pairs_bam.pairs Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,2503 @@\n+## pairs format v1.0.0\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @HD\tVN:1.6\tSO:coordinate\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\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/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.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:1.0.3\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/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.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:1.0.3\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/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.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:1.0.3\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:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:samtools\tVN:1.0.3\n+#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2\n+HWI-ST560:29:B0A7L'..b"59\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2950:12599\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2950:12599\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGCAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19?1//177787@C@C@CCC@@@@@@@@@CC@@@@@CC\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2950:12599\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19%+++,200/-<:<<<:::::<<<:<@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2962:14389\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2962:14389\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CCTCAATGATATTCGAATACGCTTTGAGGAGATACA\x19B553387877C@C@CCC@CCC@CC@C@C@@@@@CC@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2962:14389\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NAACCGAAATACATACATTGTCTTCCGTAAAGCGCT\x19)333388888C@CC@@CCC@C@@CC@@CCCC@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2969:19460\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2969:19460\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CGCTTTTCTTCCGATTATTCTTTATAATAACATCAG\x19?3333988222CCCCC@@C@C@22@CC@CCC@@@@C\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2969:19460\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NCCGATAACTAACTTAGTTAATATGGTATAAGTAAC\x19)333387787CC@CCCC@CCC@@C@CC@@@@@C@C@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2980:21055\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2980:21055\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGAAGAGCGGTTCAGCAGGAATGACGAGACCG\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2980:21055\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2984:14071\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2984:14071\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B333377777C@C@@@@C@@@@@@C@@CC@@@@C@C\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2984:14071\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19'000355443@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2986:9332\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2986:9332\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19D555577777@@CCCCC@@@@C@@C@@@@C@@@CC@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2986:9332\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&/--/35353@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:3015:8059\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3015:8059\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19AATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19,/2//66663@@C@@@CC@C@@C@C@C@CC;C@CCC\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3015:8059\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&,),)../.-@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:3037:8697\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3037:8697\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19-333377777C@C@C@CC@@@@C@@@C@CC@@C@C@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3037:8697\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19'-///35333@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\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:1:1:3057:21304\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" |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_parsed_pairs_bam_5unique.pairs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_parsed_pairs_bam_5unique.pairs Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,2503 @@\n+## pairs format v1.0.0\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @HD\tVN:1.6\tSO:coordinate\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\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/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\tPP:bwa\tVN:1.0.3\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/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\tPP:bwa-2CCE5976\tVN:1.0.3\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/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\tPP:bwa-3CAFD9D9\tVN:1.0.3\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:/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\tPP:samtools\tVN:1.0.3\n+#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2'..b"59\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2950:12599\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2950:12599\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGCAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19?1//177787@C@C@CCC@@@@@@@@@CC@@@@@CC\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2950:12599\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19%+++,200/-<:<<<:::::<<<:<@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2962:14389\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2962:14389\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CCTCAATGATATTCGAATACGCTTTGAGGAGATACA\x19B553387877C@C@CCC@CCC@CC@C@C@@@@@CC@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2962:14389\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NAACCGAAATACATACATTGTCTTCCGTAAAGCGCT\x19)333388888C@CC@@CCC@C@@CC@@CCCC@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2969:19460\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2969:19460\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CGCTTTTCTTCCGATTATTCTTTATAATAACATCAG\x19?3333988222CCCCC@@C@C@22@CC@CCC@@@@C\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2969:19460\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NCCGATAACTAACTTAGTTAATATGGTATAAGTAAC\x19)333387787CC@CCCC@CCC@@C@CC@@@@@C@C@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2980:21055\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2980:21055\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGAAGAGCGGTTCAGCAGGAATGACGAGACCG\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2980:21055\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2984:14071\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2984:14071\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B333377777C@C@@@@C@@@@@@C@@CC@@@@C@C\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2984:14071\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19'000355443@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2986:9332\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2986:9332\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19D555577777@@CCCCC@@@@C@@C@@@@C@@@CC@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2986:9332\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&/--/35353@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:3015:8059\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3015:8059\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19AATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19,/2//66663@@C@@@CC@C@@C@C@C@CC;C@CCC\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3015:8059\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&,),)../.-@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:3037:8697\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3037:8697\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19-333377777C@C@C@CC@@@@C@@@C@CC@@C@C@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3037:8697\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19'-///35333@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\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:1:1:3057:21304\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" |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_parsed_pairs_bam_min_mapq_40.pairs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_parsed_pairs_bam_min_mapq_40.pairs Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,2503 @@\n+## pairs format v1.0.0\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @HD\tVN:1.6\tSO:coordinate\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\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/tmpvtvmbj0m/files/5/0/f/dataset_50f1299b-3b0f-4a0a-ae1e-e09b66e47369.dat -c /tmp/tmpvtvmbj0m/files/7/5/c/dataset_75c85deb-b408-42ff-90f5-5cea61a9594f.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/11/outputs/dataset_04ba0223-4885-4724-847b-02525a7ef606.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:1.0.3\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/tmpvtvmbj0m/files/5/0/f/dataset_50f1299b-3b0f-4a0a-ae1e-e09b66e47369.dat -c /tmp/tmpvtvmbj0m/files/7/5/c/dataset_75c85deb-b408-42ff-90f5-5cea61a9594f.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/11/outputs/dataset_04ba0223-4885-4724-847b-02525a7ef606.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:1.0.3\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/tmpvtvmbj0m/files/5/0/f/dataset_50f1299b-3b0f-4a0a-ae1e-e09b66e47369.dat -c /tmp/tmpvtvmbj0m/files/7/5/c/dataset_75c85deb-b408-42ff-90f5-5cea61a9594f.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/11/outputs/dataset_04ba0223-4885-4724-847b-02525a7ef606.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:1.0.3\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:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/0/f/dataset_50f1299b-3b0f-4a0a-ae1e-e09b66e47369.dat -c /tmp/tmpvtvmbj0m/files/7/5/c/dataset_75c85deb-b408-42ff-90f5-5cea61a9594f.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/11/outputs/dataset_04ba0223-4885-4724-847b-02525a7ef606.dat --min-mapq 40 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:samtools\tVN:1.0.3\n+#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2\n+HWI-ST560:'..b"59\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2950:12599\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2950:12599\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGCAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19?1//177787@C@C@CCC@@@@@@@@@CC@@@@@CC\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2950:12599\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19%+++,200/-<:<<<:::::<<<:<@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2962:14389\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2962:14389\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CCTCAATGATATTCGAATACGCTTTGAGGAGATACA\x19B553387877C@C@CCC@CCC@CC@C@C@@@@@CC@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2962:14389\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NAACCGAAATACATACATTGTCTTCCGTAAAGCGCT\x19)333388888C@CC@@CCC@C@@CC@@CCCC@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2969:19460\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2969:19460\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CGCTTTTCTTCCGATTATTCTTTATAATAACATCAG\x19?3333988222CCCCC@@C@C@22@CC@CCC@@@@C\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2969:19460\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NCCGATAACTAACTTAGTTAATATGGTATAAGTAAC\x19)333387787CC@CCCC@CCC@@C@CC@@@@@C@C@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2980:21055\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2980:21055\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGAAGAGCGGTTCAGCAGGAATGACGAGACCG\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2980:21055\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2984:14071\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2984:14071\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B333377777C@C@@@@C@@@@@@C@@CC@@@@C@C\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2984:14071\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19'000355443@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:2986:9332\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2986:9332\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19D555577777@@CCCCC@@@@C@@C@@@@C@@@CC@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2986:9332\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&/--/35353@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:3015:8059\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3015:8059\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19AATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19,/2//66663@@C@@@CC@C@@C@C@C@CC;C@CCC\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3015:8059\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&,),)../.-@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+HWUSI-EAS1533_0033_FC:1:1:3037:8697\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3037:8697\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19-333377777C@C@C@CC@@@@C@@@C@CC@@C@C@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3037:8697\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19'-///35333@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\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:1:1:3057:21304\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" |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_parsed_pairs_bam_readid_dropped.pairs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_parsed_pairs_bam_readid_dropped.pairs Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,2503 @@\n+## pairs format v1.0.0\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @HD\tVN:1.6\tSO:coordinate\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\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/tmpvtvmbj0m/files/d/5/3/dataset_d53eccb1-028d-443e-aa5b-fb883976b07e.dat -c /tmp/tmpvtvmbj0m/files/d/c/c/dataset_dcc72f04-07a7-4159-8ecd-c8b978775fa1.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/19/outputs/dataset_86720212-8079-41ce-a66f-37e5222dc3ff.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:1.0.3\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/tmpvtvmbj0m/files/d/5/3/dataset_d53eccb1-028d-443e-aa5b-fb883976b07e.dat -c /tmp/tmpvtvmbj0m/files/d/c/c/dataset_dcc72f04-07a7-4159-8ecd-c8b978775fa1.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/19/outputs/dataset_86720212-8079-41ce-a66f-37e5222dc3ff.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:1.0.3\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/tmpvtvmbj0m/files/d/5/3/dataset_d53eccb1-028d-443e-aa5b-fb883976b07e.dat -c /tmp/tmpvtvmbj0m/files/d/c/c/dataset_dcc72f04-07a7-4159-8ecd-c8b978775fa1.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/19/outputs/dataset_86720212-8079-41ce-a66f-37e5222dc3ff.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:1.0.3\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:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/d/5/3/dataset_d53eccb1-028d-443e-aa5b-fb883976b07e.dat -c /tmp/tmpvtvmbj0m/files/d/c/c/dataset_dcc72f04-07a7-4159-8ecd-c8b978775fa1.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/19/outputs/dataset_86720212-8079-41ce-a66f-37e5222dc3ff.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:samtools\tVN:1.0.3\n+#columns: readID chr'..b"@@@CCC@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2941:12013\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19'--//77777@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2948:5859\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19+)*)*----+@@@@@@@@@@:::::5888877999@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2948:5859\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2950:12599\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGCAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19?1//177787@C@C@CCC@@@@@@@@@CC@@@@@CC\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2950:12599\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19%+++,200/-<:<<<:::::<<<:<@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2962:14389\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CCTCAATGATATTCGAATACGCTTTGAGGAGATACA\x19B553387877C@C@CCC@CCC@CC@C@C@@@@@CC@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2962:14389\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NAACCGAAATACATACATTGTCTTCCGTAAAGCGCT\x19)333388888C@CC@@CCC@C@@CC@@CCCC@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2969:19460\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CGCTTTTCTTCCGATTATTCTTTATAATAACATCAG\x19?3333988222CCCCC@@C@C@22@CC@CCC@@@@C\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2969:19460\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NCCGATAACTAACTTAGTTAATATGGTATAAGTAAC\x19)333387787CC@CCCC@CCC@@C@CC@@@@@C@C@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2980:21055\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGAAGAGCGGTTCAGCAGGAATGACGAGACCG\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2980:21055\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19####################################\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2984:14071\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19B333377777C@C@@@@C@@@@@@C@@CC@@@@C@C\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2984:14071\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19'000355443@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:2986:9332\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19CATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19D555577777@@CCCCC@@@@C@@C@@@@C@@@CC@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:2986:9332\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&/--/35353@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3015:8059\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19AATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19,/2//66663@@C@@@CC@C@@C@C@C@CC;C@CCC\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3015:8059\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19&,),)../.-@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\n+.\t!\t0\t!\t0\t-\t-\tNN\tHWUSI-EAS1533_0033_FC:1:1:3037:8697\x1977\x19*\x190\x190\x19*\x19*\x190\x190\x19TATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG\x19-333377777C@C@C@CC@@@@C@@@C@CC@@C@C@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\tHWUSI-EAS1533_0033_FC:1:1:3037:8697\x19141\x19*\x190\x190\x19*\x19*\x190\x190\x19NATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\x19'-///35333@@@@@@@@@@@@@@@@@@@@@@@@@@\x19AS:i:0\x19XS:i:0\x19Yt:Z:NN\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+.\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" |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_parsed_pairs_bam_readid_dropped_seq.pairs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_parsed_pairs_bam_readid_dropped_seq.pairs Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,600 @@\n+## pairs format v1.0.0\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: Test_seq 450060\n+#samheader: @SQ\tSN:Test_seq\tLN:450060\n+#samheader: @PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SP -T0 -t 8 test test_hic_reads_1.fq test_hic_reads_2.fq\n+#samheader: @PG\tID:pairtools_parse\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/6/d/e/dataset_6dee055e-91e3-4fb7-a2cb-65bb836b6b46.dat -c /tmp/tmpvtvmbj0m/files/f/6/d/dataset_f6d93a5f-aa4c-4b78-802c-e7b94fcee3e4.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/22/outputs/dataset_6d40908c-8b00-4098-8c50-3c42836de0ee.dat --min-mapq 40 --max-molecule-size 750 --drop-seq --walks-policy 5unique --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-mem2\tVN:1.0.3\n+#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2\n+A00126:224:H7HMWDSX3:3:1101:4779:3098\t!\t0\tTest_seq\t166211\t-\t-\tMU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19177\x19Test_seq\x19214824\x195\x1978M\x19=\x19166134\x19-48691\x19*\x19*\x19NM:i:3\x19MD:Z:1T33G33A8\x19MC:Z:78M\x19AS:i:66\x19XS:i:63\x19XA:Z:Test_seq,+166134,78M,3;\x19Yt:Z:MU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19113\x19Test_seq\x19166134\x1943\x1978M\x19=\x19214824\x1948691\x19*\x19*\x19NM:i:0\x19MD:Z:78\x19MC:Z:78M\x19AS:i:78\x19XS:i:63\x19XA:Z:Test_seq,+214829,5S73M,2;\x19Yt:Z:MU\n+A00126:224:H7HMWDSX3:3:1101:2908:3239\t!\t0\tTest_seq\t167696\t-\t-\tMU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x19161\x19Test_seq\x19167331\x1923\x19151M\x19=\x19167546\x19366\x19*\x19*\x19NM:i:1\x19MD:Z:37A113\x19MC:Z:151M\x19AS:i:146\x19XS:i:135\x19XA:Z:Test_seq,-213553,151M,4;\x19Yt:Z:MU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x1981\x19Test_seq\x19167546\x1944\x19151M\x19=\x19167331\x19-366\x19*\x19*\x19NM:i:3\x19MD:Z:82G15T30C21\x19MC:Z:151M\x19AS:i:136\x19XS:i:114\x19XA:Z:Test_seq,+213342,118M2I23M2I6M,8;\x19Yt:Z:MU\n+A00126:224:H7HMWDSX3:3:1101:27208:4492\tTest_seq\t194620\tTest_seq\t194909\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x1997\x19Test_seq\x19194620\x1960\x19151M\x19=\x19194778\x19290\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:132M19S\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x19145\x19Test_seq\x19194778\x1960\x19132M19S\x19=\x19194620\x19-290\x19*\x19*\x19NM:i:0\x19MD:Z:132\x19MC:Z:151M\x19AS:i:132\x19XS:i:0\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1101:9344:5306\t!\t0\t!\t0\t-\t-\tMM\tA00126:224:H7HMWDSX3:3:1101:9344:5306\x1997\x19Test_seq\x19449503\x197\x1960M\x19=\x19449503\x1960\x19*\x19*\x19NM:i:4\x19MD:Z:3T44G2C5G2\x19MC:Z:60M\x19AS:i:44\x19XS:i:40\x19XA:Z:Test_seq,+16926,60M,5;\x19Yt:Z:MM\tA00126:224:H7HMWDSX3:3:1101:9344:5306\x19145\x19Test_seq\x19449503\x1912\x1960M\x19=\x19449503\x19-60\x19*\x19*\x19NM:i:1\x19MD:Z:53T6\x19MC:Z:60M\x19AS:i:55\x19XS:i:50\x19XA:Z:Test_seq,-16926,60M,2;\x19Yt:Z:MM\n+A00126:224:H7HMWDSX3:3:1101:17607:5212\tTest_seq\t83425\tTest_seq\t93852\t-\t+\tUR\tA00126:224:H7HMWDSX3:3:1101:17607:5212\x1981\x19Test_seq\x1983397\x1960\x19122S29M\x19=\x1993852\x1910428\x19*\x19*\x19NM:i:0\x19MD:Z:29\x19MC:Z:151M\x19AS:i:29\x19XS:i:0\x19SA:Z:Test_seq,94155,-,122M29S,60,0;\x19Yt:Z:UR\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1101:17607:5212\x192129\x19Test_seq\x1994155\x1960\x19122M29H\x19=\x1993852\x19-425\x19*\x19*\x19NM:i:0\x19MD:Z:122\x19MC:Z:151M\x19AS:i:122\x19XS:i:0\x19SA:Z:Test_seq,83397,-,122S29M,60,0;\x19Yt:Z:UR\tA00126:224:H7HMWDSX3:3:1101:17607:5212\x19161\x19Test_seq\x1993852\x1960\x19151M\x19=\x1983397\x19-10428\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:122S29M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UR\n+A00126:224:H7HMWDSX3:3:1101:17942:7263\tTest_seq\t168528\tTest_seq\t168867\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:17942:7263\x1997\x19Test_seq\x19168528\x1960\x19151M\x19=\x19168717\x19340\x19*\x19*\x19NM:i:5\x19MD:Z:12A68A23T2A26T15\x19MC:Z:151M\x19AS:i:126\x19XS:i:91\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:17942:7263\x19145\x19Test_seq\x19168717\x1960\x19151M\x19=\x19168528\x19-340\x19*\x19*\x19NM:i:1\x19MD:Z:27G123\x19MC:Z:151M\x19AS:i:146\x19XS:i:91\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1101:5683:8108\t!\t0\tTest_seq\t170834\t-\t+\tMR\tA00126:224:H7HMWDSX3:3:1101:5683:8108\x1965\x19Test_seq\x19137032\x190\x1928M123S\x19=\x19170834\x1933803\x19*\x19*\x19NM:i:1\x19MD:Z:7G20\x19MC:Z:151M\x19AS:i:23\x19XS:i:23\x19SA:Z:Test_seq,171170,-,119M32S,60,0;\x19XA:Z:Test_seq,+333108,28M123S,1;Test_seq,-298750,123S26M2S,1;Test_seq,-279319,123S28M,2;\x19Yt:Z:MR\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1101:5683:8108\x192129\x19Test_seq\x19171170\x1960\x19119M32H\x19=\x19170834\x19-455\x19*\x19*\x19NM:i:0\x19MD:Z:119\x19MC:Z:151M\x19AS:i:119\x19XS:i:0\x19SA:Z:Test_seq,137032,+,28M123S,0,1;\x19Yt:Z:MR\tA00126:224:H7HMWDSX3:3:1101:5683:8108\x19129\x19Test_seq\x19170834\x1960\x19151M\x19=\x19137032\x19-33803\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:28M123S\x19AS:i:151\x19XS:i:0\x19Yt:Z:MR\n+A00126:22'..b'est_seq\t165792\tTest_seq\t166199\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:9525:1548\x19161\x19Test_seq\x19165792\x1960\x19110M2D41M\x19=\x19166049\x19408\x19*\x19*\x19NM:i:12\x19MD:Z:2A5T9T13C31A10A8G11A13^CC7G19T13\x19MC:Z:151M\x19AS:i:95\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:9525:1548\x1981\x19Test_seq\x19166049\x1960\x19151M\x19=\x19165792\x19-408\x19*\x19*\x19NM:i:1\x19MD:Z:53G97\x19MC:Z:110M2D41M\x19AS:i:146\x19XS:i:50\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1116:28917:2190\tTest_seq\t74270\tTest_seq\t74579\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:28917:2190\x1997\x19Test_seq\x1974270\x1960\x19151M\x19=\x1974429\x19310\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:151M\x19AS:i:151\x19XS:i:41\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:28917:2190\x19145\x19Test_seq\x1974429\x1960\x19151M\x19=\x1974270\x19-310\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:151M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1116:3495:3724\tTest_seq\t335700\tTest_seq\t436771\t-\t-\tUR\tA00126:224:H7HMWDSX3:3:1116:3495:3724\x19177\x19Test_seq\x19335669\x1960\x19119S32M\x19=\x19436621\x19101072\x19*\x19*\x19NM:i:0\x19MD:Z:32\x19MC:Z:151M\x19AS:i:32\x19XS:i:0\x19SA:Z:Test_seq,436401,+,32S119M,60,0;\x19Yt:Z:UR\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1116:3495:3724\x192209\x19Test_seq\x19436401\x1960\x1932H119M\x19=\x19436621\x19371\x19*\x19*\x19NM:i:0\x19MD:Z:119\x19MC:Z:151M\x19AS:i:119\x19XS:i:0\x19SA:Z:Test_seq,335669,-,119S32M,60,0;\x19Yt:Z:UR\tA00126:224:H7HMWDSX3:3:1116:3495:3724\x19113\x19Test_seq\x19436621\x1960\x19151M\x19=\x19335669\x19-101072\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:119S32M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UR\n+A00126:224:H7HMWDSX3:3:1116:1886:5885\tTest_seq\t133235\tTest_seq\t133657\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:1886:5885\x1997\x19Test_seq\x19133235\x1960\x19151M\x19=\x19133507\x19423\x19*\x19*\x19NM:i:1\x19MD:Z:36C114\x19MC:Z:151M\x19AS:i:146\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:1886:5885\x19145\x19Test_seq\x19133507\x1960\x19151M\x19=\x19133235\x19-423\x19*\x19*\x19NM:i:5\x19MD:Z:12G29T70C20C2C13\x19MC:Z:151M\x19AS:i:126\x19XS:i:0\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1116:5041:6715\tTest_seq\t168462\tTest_seq\t168810\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:5041:6715\x1997\x19Test_seq\x19168462\x1960\x19151M\x19=\x19168674\x19349\x19*\x19*\x19NM:i:1\x19MD:Z:33T117\x19MC:Z:137M14S\x19AS:i:146\x19XS:i:91\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:5041:6715\x19145\x19Test_seq\x19168674\x1960\x19137M14S\x19=\x19168462\x19-349\x19*\x19*\x19NM:i:5\x19MD:Z:42T10T2C7A19G52\x19MC:Z:151M\x19AS:i:112\x19XS:i:30\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1116:31720:7545\t!\t0\tTest_seq\t303522\t-\t+\tMR\tA00126:224:H7HMWDSX3:3:1116:31720:7545\x1965\x19Test_seq\x19305328\x196\x1920M131S\x19=\x19303522\x19-1807\x19*\x19*\x19NM:i:0\x19MD:Z:20\x19MC:Z:151M\x19AS:i:20\x19XS:i:0\x19SA:Z:Test_seq,303836,-,131M20S,60,0;\x19Yt:Z:MR\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1116:31720:7545\x192129\x19Test_seq\x19303836\x1960\x19131M20H\x19=\x19303522\x19-445\x19*\x19*\x19NM:i:0\x19MD:Z:131\x19MC:Z:151M\x19AS:i:131\x19XS:i:43\x19SA:Z:Test_seq,305328,+,20M131S,6,0;\x19Yt:Z:MR\tA00126:224:H7HMWDSX3:3:1116:31720:7545\x19129\x19Test_seq\x19303522\x1960\x19151M\x19=\x19305328\x191807\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:20M131S\x19AS:i:151\x19XS:i:0\x19Yt:Z:MR\n+A00126:224:H7HMWDSX3:3:1116:30870:8296\tTest_seq\t169295\tTest_seq\t169732\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:30870:8296\x1997\x19Test_seq\x19169295\x1960\x19151M\x19=\x19169582\x19438\x19*\x19*\x19NM:i:1\x19MD:Z:14T136\x19MC:Z:151M\x19AS:i:146\x19XS:i:107\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:30870:8296\x19145\x19Test_seq\x19169582\x1960\x19151M\x19=\x19169295\x19-438\x19*\x19*\x19NM:i:3\x19MD:Z:46T11A22G69\x19MC:Z:151M\x19AS:i:136\x19XS:i:22\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1116:5186:8719\t!\t0\tTest_seq\t169344\t-\t+\tNR\tA00126:224:H7HMWDSX3:3:1116:5186:8719\x1981\x19Test_seq\x19169618\x1960\x19129M22S\x19=\x19169344\x19-403\x19*\x19*\x19NM:i:5\x19MD:Z:10T11A22G70A3T8\x19MC:Z:151M\x19AS:i:104\x19XS:i:0\x19Yt:Z:NR\tA00126:224:H7HMWDSX3:3:1116:5186:8719\x19161\x19Test_seq\x19169344\x1960\x19151M\x19=\x19169618\x19403\x19*\x19*\x19NM:i:1\x19MD:Z:123G27\x19MC:Z:129M22S\x19AS:i:146\x19XS:i:101\x19Yt:Z:NR\n+A00126:224:H7HMWDSX3:3:1116:11080:9690\tTest_seq\t171531\tTest_seq\t171917\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:11080:9690\x1997\x19Test_seq\x19171531\x1960\x19151M\x19=\x19171767\x19387\x19*\x19*\x19NM:i:6\x19MD:Z:22C29T16C6T6G47G19\x19MC:Z:151M\x19AS:i:121\x19XS:i:53\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:11080:9690\x19145\x19Test_seq\x19171767\x1960\x19151M\x19=\x19171531\x19-387\x19*\x19*\x19NM:i:0\x19MD:Z:151\x19MC:Z:151M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1116:31367:10222\tTest_seq\t168346\tTest_seq\t168601\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:31367:10222\x1997\x19Test_seq\x19168346\x1960\x19130M\x19=\x19168472\x19256\x19*\x19*\x19NM:i:7\x19MD:Z:0G18A14C0C5G22C54C10\x19MC:Z:130M\x19AS:i:99\x19XS:i:40\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:31367:10222\x19145\x19Test_seq\x19168472\x1960\x19130M\x19=\x19168346\x19-256\x19*\x19*\x19NM:i:0\x19MD:Z:130\x19MC:Z:130M\x19AS:i:130\x19XS:i:75\x19Yt:Z:UU\n' |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_parsed_pairs_sam.pairs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_parsed_pairs_sam.pairs Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,600 @@\n+## pairs format v1.0.0\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: Test_seq 450060\n+#samheader: @SQ\tSN:Test_seq\tLN:450060\n+#samheader: @PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SP -T0 -t 8 test test_hic_reads_1.fq test_hic_reads_2.fq\n+#samheader: @PG\tID:pairtools_parse\tPN:pairtools_parse\tCL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/1/f/1/dataset_1f1b27bb-444f-4f9a-b79d-0addfd198f84.dat -c /tmp/tmpvtvmbj0m/files/a/6/c/dataset_a6c25687-079e-4e5f-a858-96e64dab4aff.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/3/outputs/dataset_4f9f5c5c-4d65-4e66-9fd4-61c5ab9be509.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1\tPP:bwa-mem2\tVN:1.0.3\n+#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2\n+A00126:224:H7HMWDSX3:3:1101:4779:3098\tTest_seq\t166211\tTest_seq\t214901\t-\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19113\x19Test_seq\x19166134\x1943\x1978M\x19=\x19214824\x1948691\x19GGGCACCAACTAGTTCTTCTGGTCTCAGGATAATGTAGGTCTCTGGTTCATGTGGCCCTTTCTGTCTCTTGGGTTCTT\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:78\x19MC:Z:78M\x19AS:i:78\x19XS:i:63\x19XA:Z:Test_seq,+214829,5S73M,2;\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:4779:3098\x19177\x19Test_seq\x19214824\x195\x1978M\x19=\x19166134\x19-48691\x19AAGAGCCCAAGAGACAGAAAGGGCCACATGAACCACAGACCTACATCATCCTGAGACCAGAAGAACTAGTTGGTGCCC\x19FFFF,FFFFFFFFFFFFF,FFFFFFFFFFFF:FF:,FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF\x19NM:i:3\x19MD:Z:1T33G33A8\x19MC:Z:78M\x19AS:i:66\x19XS:i:63\x19XA:Z:Test_seq,+166134,78M,3;\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1101:2908:3239\tTest_seq\t167331\tTest_seq\t167696\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x19161\x19Test_seq\x19167331\x1923\x19151M\x19=\x19167546\x19366\x19TGAGATGTCATAGCTGAATATTCTTTCCCAGTCTGTAGGTGGTCTTTTTACTCTTTTGGTGAAGTCTTTAGATGAGCATAGGTGTTTGATTTTTAGGAGCTCCCAGTTATCTGGTTTCTCTTCATCATTTTTGGTAATGTTTTGTATTCTG\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFF:FFFFF:FFFF:FFFFFFFFFFFFFFF:FF,,FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF:FFFFFFFF:FF,FF\x19NM:i:1\x19MD:Z:37A113\x19MC:Z:151M\x19AS:i:146\x19XS:i:135\x19XA:Z:Test_seq,-213553,151M,4;\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:2908:3239\x1981\x19Test_seq\x19167546\x1944\x19151M\x19=\x19167331\x19-366\x19TAGTCTTTATGTTTAGGTCTTTGATCCACTTGGAGTTAGTTTTTGTGCATGGTGTGAGGTATGGGTCCTGTTTCATTCTTTTACAAATGGATATCCAGGTATGCCAGCACCATTTGTTAAAAAGACTATTATTTCCCCAATTGACTGACAC\x19FF,F,F:FFFFFFFFF,FFF:FFFFFF:FFFF:FFFFFFFFFFF:FF::F,FFFFFFFFF:,F,FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FFF::FFFFFFFFFFFFF,FFFFFFF:FF:F,:FFFFFFFFFF,F,F:FFFFFFFFFF\x19NM:i:3\x19MD:Z:82G15T30C21\x19MC:Z:151M\x19AS:i:136\x19XS:i:114\x19XA:Z:Test_seq,+213342,118M2I23M2I6M,8;\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1101:27208:4492\tTest_seq\t194620\tTest_seq\t194909\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x1997\x19Test_seq\x19194620\x1960\x19151M\x19=\x19194778\x19290\x19GCTGTGCAAACCACTGCTCCAGGCTATCTCAGCACTGAGCCAGAGACAAGGGCCAGTTCAGTCACCTGGAAAATCAGGCCAGCATCTCTGAAAAATAGGTGCCTCAGTGTTCACAGAAAAGGGCCATGTATTGAAGTAGGTCAGAGGAAGA\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:F,FF:::FFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:151\x19MC:Z:132M19S\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:27208:4492\x19145\x19Test_seq\x19194778\x1960\x19132M19S\x19=\x19194620\x19-290\x19CACTCACCAGATTCAGCCCAGGACCAGAGGCTGCCGAGGGCAGGTGTGGGACGAAGTCAAGATGAAGTCAGTTCATTGTGTGGTTTTCGGTACCAGGCTAGACCTAGATTTGAACCCCAAGTCTGCTACTTAGATCATTCATTCAATGTGT\x19FFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:132\x19MC:Z:151M\x19AS:i:132\x19XS:i:0\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1101:9344:5306\tTest_seq\t449503\tTest_seq\t449562\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1101:9344:5306\x1997\x19Test_seq\x19449503\x197\x1960M\x19=\x19449503\x1960\x19GTTCGGACAGAACAAGGGGATACTGATTGGTTTAAAGTCAGGAAAGGTATGAGTCAGTGT\x19,FFFF,FFF:FF,FF:FF:FF:F:,F::,FF:,FFFFFFFF::FF,,:FFF,FFF::,F,\x19NM:i:4\x19MD:Z:3T44G2C5G2\x19MC:Z:60M\x19AS:i:44\x19XS:i:40\x19XA:Z:Test_seq,+16926,60M,5;\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1101:9344:5306\x19145\x19Test_seq\x19449503\x1912\x1960M\x19=\x19449503\x19-60\x19GTTTGGACAGAACAAGG'..b'i:0\x19SA:Z:Test_seq,303836,-,131M20S,60,0;\x19Yt:Z:RU\x19NEXT_SAM\x19A00126:224:H7HMWDSX3:3:1116:31720:7545\x192129\x19Test_seq\x19303836\x1960\x19131M20H\x19=\x19303522\x19-445\x19ATGAAACACTGCCCAGCCCTGCGCCATCCTCACAGTTGTTGTTATGCTTGAGCCCATTGTTGCAGCCACTGTGTCAATCCATGTTGGCCCTCTACTTTACCAAGCATGATGTCCTTCTCCAGGGAGTGATC\x19FFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:F,FFFFFFFFFFFFFFF:FFFFFF::F,FFFFFFFFF:F:FFFFF:FFF:FF:FFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:131\x19MC:Z:151M\x19AS:i:131\x19XS:i:43\x19SA:Z:Test_seq,305328,+,20M131S,6,0;\x19Yt:Z:RU\n+A00126:224:H7HMWDSX3:3:1116:30870:8296\tTest_seq\t169295\tTest_seq\t169732\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:30870:8296\x1997\x19Test_seq\x19169295\x1960\x19151M\x19=\x19169582\x19438\x19GTTTCCTTTCCTGTATTTCTTTAGTCAGTCTAGCCAATGGTTTATCAATTTTGTTAATTTTTTCAAAGAACCAGCTTTTGGCTTTGTTAATTCTTTCAATTGTTTTTCTGTTCTCTAATTCATTTAGTTCAGCTCTAATTTTTATTATTTG\x19FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFF:FFFFFFF:FFF:F:FFFFFFFF:F:F:FFFFFFFFFFF:FFFFFFF,FFFFF:FFFF:F,FFFFFFFFFFFF\x19NM:i:1\x19MD:Z:14T136\x19MC:Z:151M\x19AS:i:146\x19XS:i:107\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:30870:8296\x19145\x19Test_seq\x19169582\x1960\x19151M\x19=\x19169295\x19-438\x19GCTTTTGCTGTGTCCCAGAGGTTTTGATAGGAAGTATTTTCATTCTCGTTGCTTTCTATGAATTTCCTTATTCCCTCCTTGATGTCTTCTATAACCCAGTCTTTTTTCAGGAGGGTATTGTTCATTTTCCAAGTATTTGATTTCTTTTCCC\x19:FFF:FFFFFFFFF,:FFF,FFFFF:FFFFFFF:FFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:\x19NM:i:3\x19MD:Z:46T11A22G69\x19MC:Z:151M\x19AS:i:136\x19XS:i:22\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1116:5186:8719\t!\t0\tTest_seq\t169344\t-\t+\tNR\tA00126:224:H7HMWDSX3:3:1116:5186:8719\x1981\x19Test_seq\x19169618\x1960\x19129M22S\x19=\x19169344\x19-403\x19TTTTCATTCTCGTTGCTTTCTATGAATTTCCTTATTCCCTCCTTGATGTCTTCTATAACCCAGTCTTTTTTCAGGAGGGTATTGTTCATTTTCCAAGTATTTGATTTCTTTTCCCTCGTTCTTCTGTTATTGATCGATCTGTCATACTCTG\x19F:FFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFF:FFF:FFFFFFFFFFF\x19NM:i:5\x19MD:Z:10T11A22G70A3T8\x19MC:Z:151M\x19AS:i:104\x19XS:i:0\x19Yt:Z:NR\tA00126:224:H7HMWDSX3:3:1116:5186:8719\x19161\x19Test_seq\x19169344\x1960\x19151M\x19=\x19169618\x19403\x19TTTGTTAATTTTTTCAAAGAACCAGCTTTTGGCTTTGTTAATTCTTTCAATTGTTTTTCTGTTCTCTAATTCATTTAGTTCAGCTCTAATTTTTATTATTTGTTTTCTTCTGGTGCCTGATGGATTCTTTTGTTGCTCACTTTCTATTTGT\x19FFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF,FFFFF:FFFF:FFFF,FF:FFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFF,FFFFFFFF,FFF:FFFFFF,FFFFFFFFFFFFF:FFFFFFF,FFFF,F:FFFFF,FFFF,F:F,\x19NM:i:1\x19MD:Z:123G27\x19MC:Z:129M22S\x19AS:i:146\x19XS:i:101\x19Yt:Z:NR\n+A00126:224:H7HMWDSX3:3:1116:11080:9690\tTest_seq\t171531\tTest_seq\t171917\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:11080:9690\x1997\x19Test_seq\x19171531\x1960\x19151M\x19=\x19171767\x19387\x19TTCCCTGGTCCTCCAGAAGTCCTAGTCTACATTCTAATTGCTCGAGTCTGCTCCTCTGACTTTCTATTGTGTTGTCAAATTCTATAATTTTATTGTTAATCTTTTGGATTTCTACATGCTGTCTCTCTATGTATTCTTGCAACTTATTAAT\x19FFFFFFF:F,FFFFFFFFFF::FFFFFFFFFF:FFFFFFF:FF:F:F,FFFFFFFF:F:::,FFFF:FFFFFFFFFFF,FF:FFF:F,:FFFFFFF:,FFFFFFF::FFF:FF:F,:F,,F:::F,:FFFFF,FF,FFF,,F,:FFFFF:F\x19NM:i:6\x19MD:Z:22C29T16C6T6G47G19\x19MC:Z:151M\x19AS:i:121\x19XS:i:53\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:11080:9690\x19145\x19Test_seq\x19171767\x1960\x19151M\x19=\x19171531\x19-387\x19ATTTCATTTGTGATATCTTTAAGCATTCTGTAAATTAGTTTTTTATATTCTGTATCTGATAATTCCAGGATTGTATCTTCATTTGGGAAAGATTTTGATTCTTTTGTTTGGGGGGTTGGAGAAGCTGTCATGGTCTGTTTCTTTATGTGGT\x19FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF,F:FFFFF::FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF\x19NM:i:0\x19MD:Z:151\x19MC:Z:151M\x19AS:i:151\x19XS:i:0\x19Yt:Z:UU\n+A00126:224:H7HMWDSX3:3:1116:31367:10222\tTest_seq\t168346\tTest_seq\t168601\t+\t-\tUU\tA00126:224:H7HMWDSX3:3:1116:31367:10222\x1997\x19Test_seq\x19168346\x1960\x19130M\x19=\x19168472\x19256\x19ATCATGTCATCTGCAAATAGTGATAGCTTTACTTTGTCCTTACCAATCTGGATACCCTTTATTTTTTTGTCTAGCCTAATTGCCCTGGCTAGGACTTCAAGTACGATGTTGAATAAGAGTGGTGATAAAG\x19*\x19NM:i:7\x19MD:Z:0G18A14C0C5G22C54C10\x19MC:Z:130M\x19AS:i:99\x19XS:i:40\x19Yt:Z:UU\tA00126:224:H7HMWDSX3:3:1116:31367:10222\x19145\x19Test_seq\x19168472\x1960\x19130M\x19=\x19168346\x19-256\x19AAAGGGCATCCTTGTCTGGTTCCTGTTCTCAAGGGAAATGCTTTCAGGTTCTCTCCATTTAGAGTGATATTGGCTGTTGGCTTTGCATAGATGCCCTTTATTATGTTGAGGAATTTTCCTTCAATTCCTA\x19*\x19NM:i:0\x19MD:Z:130\x19MC:Z:130M\x19AS:i:130\x19XS:i:75\x19Yt:Z:UU\n' |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_sorted_pairs.pairs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_sorted_pairs.pairs Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,2508 @@\n+## pairs format v1.0.0\n+#sorted: chr1-chr2-pos1-pos2\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @HD\tVN:1.6\tSO:coordinate\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\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/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.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:1.0.3\n+#samheader: @PG\tID:pairtools_sort-1.3\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/d/5/c/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/2/outputs/dataset_b446f275-b840-40de-9fb8-08bd13d19337.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-1.2\tVN:1.0.3\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/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.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:1.0.3\n+#samheader: @PG\tID:pairtools_sort-2.3\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/d/5/c/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/2/outputs/dataset_b446f275-b840-40de-9fb8-08bd13d19337.dat --nproc-in 1 --nproc-out 1\tPP:pairtools_parse-2.2\tVN:1.0.3\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/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.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:1.0.3\n+#samheader: @PG\tID:pairtools_sort-3.3\tPN:pairtools_sort\tCL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/d/5/c/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o '..b"EAS1533_0033_FC:1:1:2636:20802\x19145\x19chrXVI\x19475835\x1960\x1936M\x19=\x19475619\x19-252\x19TATAACGCGCTGAGAGCTGGTAAGAACAATAGGCCN\x19@C@@@C@C@@CC@@CC@@@@CC@@@@889996666)\x19NM:i:1\x19MD:Z:35G0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:2789:3854\tchrXVI\t548088\tchrXVI\t548271\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:2789:3854\x1997\x19chrXVI\x19548088\x1960\x1936M\x19=\x19548236\x19184\x19CTTCATTGTTTGGTGGTGAAAGCTATAGGGACGATT\x19A.2.-6665322@@@55777@@@@@C@CC@CCC@@@\x19NM:i:1\x19MD:Z:0T35\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:2789:3854\x19145\x19chrXVI\x19548236\x1960\x1936M\x19=\x19548088\x19-184\x19TTTTTCGAGTCAGAAATGATAACACTAACACAGGCN\x19@C@C@@C@C@@CC@CC@CCC@<<<<<10002,,,0&\x19NM:i:1\x19MD:Z:35T0\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:2993:3814\tchrXVI\t610391\tchrXVI\t610663\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:2993:3814\x19161\x19chrXVI\x19610391\x1960\x1936M\x19=\x19610628\x19273\x19NAAGCACAGCTTAAAGGATAAACAGGATTTTATTGA\x19)333387788CCCC@CC@CCC@@@@@C@C@@@222@\x19NM:i:1\x19MD:Z:0C35\x19AS:i:35\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:2993:3814\x1981\x19chrXVI\x19610628\x1958\x1936M\x19=\x19610391\x19-273\x19GAAAAGACTAGCGGTGAAATGCCTCCTAAGAAGGAT\x1922CCCC@C@@@@@@CC@CC@@CC@CC888883333,\x19NM:i:2\x19MD:Z:7A27A0\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\n+HWUSI-EAS1533_0033_FC:1:1:1552:8158\tchrXVI\t663679\tchrXVI\t664015\t+\t-\tUU\tHWUSI-EAS1533_0033_FC:1:1:1552:8158\x19161\x19chrXVI\x19663679\x1958\x1936M\x19=\x19663980\x19337\x19NGCTCGAATTTAGATTCATTCGGGGTAAATATTTGC\x19'../.77777C@C@C@@CCC@@@@@@@@@@@@@@@C\x19NM:i:2\x19MD:Z:0A28C6\x19AS:i:30\x19XS:i:0\x19Yt:Z:UU\tHWUSI-EAS1533_0033_FC:1:1:1552:8158\x1981\x19chrXVI\x19663980\x1960\x1936M\x19=\x19663679\x19-337\x19AGTTATACAAACTTTCTACATCAAAGCAGTACAGCT\x19@@@C@@@@CCCC@C@@@CCC@@@@@@54535../.,\x19NM:i:0\x19MD:Z:36\x19AS:i:36\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+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" |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/output_sorted_pairs.pairsam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_sorted_pairs.pairsam Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,2044 @@\n+## pairs format v1.0.0\n+#sorted: chr1-chr2-pos1-pos2\n+#shape: upper triangle\n+#genome_assembly: unknown\n+#chromsize: chrI 230218\n+#chromsize: chrII 813184\n+#chromsize: chrIII 316620\n+#chromsize: chrIV 1531933\n+#chromsize: chrV 576874\n+#chromsize: chrVI 270161\n+#chromsize: chrVII 1090940\n+#chromsize: chrVIII 562643\n+#chromsize: chrIX 439888\n+#chromsize: chrX 745751\n+#chromsize: chrXI 666816\n+#chromsize: chrXII 1078177\n+#chromsize: chrXIII 924431\n+#chromsize: chrXIV 784333\n+#chromsize: chrXV 1091291\n+#chromsize: chrXVI 948066\n+#chromsize: chrM 85779\n+#samheader: @SQ\tSN:chrI\tLN:230218\n+#samheader: @SQ\tSN:chrII\tLN:813184\n+#samheader: @SQ\tSN:chrIII\tLN:316620\n+#samheader: @SQ\tSN:chrIV\tLN:1531933\n+#samheader: @SQ\tSN:chrIX\tLN:439888\n+#samheader: @SQ\tSN:chrM\tLN:85779\n+#samheader: @SQ\tSN:chrV\tLN:576874\n+#samheader: @SQ\tSN:chrVI\tLN:270161\n+#samheader: @SQ\tSN:chrVII\tLN:1090940\n+#samheader: @SQ\tSN:chrVIII\tLN:562643\n+#samheader: @SQ\tSN:chrX\tLN:745751\n+#samheader: @SQ\tSN:chrXI\tLN:666816\n+#samheader: @SQ\tSN:chrXII\tLN:1078177\n+#samheader: @SQ\tSN:chrXIII\tLN:924431\n+#samheader: @SQ\tSN:chrXIV\tLN:784333\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:/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: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: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.reduced.chrom.sizes test.bam\tPP:bwa-3CAFD9D9\tVN:1.0.2\n+#samheader: @PG\tID:pairtools_sort-3.3\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-3.2\tVN:1.0.2\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\t'..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" |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/test.bam |
| b |
| Binary file test-data/test.bam has changed |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/test.genome --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.genome Thu Apr 04 19:40:59 2024 +0000 |
| b |
| @@ -0,0 +1,1 @@ +Test_seq 450060 |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/test.reduced.chrom.sizes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.reduced.chrom.sizes Thu Apr 04 19:40:59 2024 +0000 |
| b |
| @@ -0,0 +1,17 @@ +chrI 230218 +chrII 813184 +chrIII 316620 +chrIV 1531933 +chrV 576874 +chrVI 270161 +chrVII 1090940 +chrVIII 562643 +chrIX 439888 +chrX 745751 +chrXI 666816 +chrXII 1078177 +chrXIII 924431 +chrXIV 784333 +chrXV 1091291 +chrXVI 948066 +chrM 85779 |
| b |
| diff -r 000000000000 -r f8c1d2a93d43 test-data/test.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.sam Thu Apr 04 19:40:59 2024 +0000 |
| b |
| b'@@ -0,0 +1,1228 @@\n+@SQ\tSN:Test_seq\tLN:450060\n+@PG\tID:bwa-mem2\tPN:bwa-mem2\tVN:2.2.1\tCL:bwa-mem2 mem -5SP -T0 -t 8 test test_hic_reads_1.fq test_hic_reads_2.fq\n+A00126:224:H7HMWDSX3:3:1101:4779:3098\t113\tTest_seq\t166134\t43\t78M\t=\t214824\t48691\tGGGCACCAACTAGTTCTTCTGGTCTCAGGATAATGTAGGTCTCTGGTTCATGTGGCCCTTTCTGTCTCTTGGGTTCTT\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFF\tNM:i:0\tMD:Z:78\tMC:Z:78M\tAS:i:78\tXS:i:63\tXA:Z:Test_seq,+214829,5S73M,2;\n+A00126:224:H7HMWDSX3:3:1101:4779:3098\t177\tTest_seq\t214824\t5\t78M\t=\t166134\t-48691\tAAGAGCCCAAGAGACAGAAAGGGCCACATGAACCACAGACCTACATCATCCTGAGACCAGAAGAACTAGTTGGTGCCC\tFFFF,FFFFFFFFFFFFF,FFFFFFFFFFFF:FF:,FFFFFFF:FF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF\tNM:i:3\tMD:Z:1T33G33A8\tMC:Z:78M\tAS:i:66\tXS:i:63\tXA:Z:Test_seq,+166134,78M,3;\n+A00126:224:H7HMWDSX3:3:1101:2908:3239\t81\tTest_seq\t167546\t44\t151M\t=\t167331\t-366\tTAGTCTTTATGTTTAGGTCTTTGATCCACTTGGAGTTAGTTTTTGTGCATGGTGTGAGGTATGGGTCCTGTTTCATTCTTTTACAAATGGATATCCAGGTATGCCAGCACCATTTGTTAAAAAGACTATTATTTCCCCAATTGACTGACAC\tFF,F,F:FFFFFFFFF,FFF:FFFFFF:FFFF:FFFFFFFFFFF:FF::F,FFFFFFFFF:,F,FFF:FFFFFFFFFFFFFFFFFFFFF:FF:FFF::FFFFFFFFFFFFF,FFFFFFF:FF:F,:FFFFFFFFFF,F,F:FFFFFFFFFF\tNM:i:3\tMD:Z:82G15T30C21\tMC:Z:151M\tAS:i:136\tXS:i:114\tXA:Z:Test_seq,+213342,118M2I23M2I6M,8;\n+A00126:224:H7HMWDSX3:3:1101:2908:3239\t161\tTest_seq\t167331\t23\t151M\t=\t167546\t366\tTGAGATGTCATAGCTGAATATTCTTTCCCAGTCTGTAGGTGGTCTTTTTACTCTTTTGGTGAAGTCTTTAGATGAGCATAGGTGTTTGATTTTTAGGAGCTCCCAGTTATCTGGTTTCTCTTCATCATTTTTGGTAATGTTTTGTATTCTG\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFF:FFFFF:FFFF:FFFFFFFFFFFFFFF:FF,,FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFF:FFFFFFFF:FF,FF\tNM:i:1\tMD:Z:37A113\tMC:Z:151M\tAS:i:146\tXS:i:135\tXA:Z:Test_seq,-213553,151M,4;\n+A00126:224:H7HMWDSX3:3:1101:27208:4492\t97\tTest_seq\t194620\t60\t151M\t=\t194778\t290\tGCTGTGCAAACCACTGCTCCAGGCTATCTCAGCACTGAGCCAGAGACAAGGGCCAGTTCAGTCACCTGGAAAATCAGGCCAGCATCTCTGAAAAATAGGTGCCTCAGTGTTCACAGAAAAGGGCCATGTATTGAAGTAGGTCAGAGGAAGA\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFF:FFFFFFFFF:F,FF:::FFFFFFFFFFFFFFFFFFF\tNM:i:0\tMD:Z:151\tMC:Z:132M19S\tAS:i:151\tXS:i:0\n+A00126:224:H7HMWDSX3:3:1101:27208:4492\t145\tTest_seq\t194778\t60\t132M19S\t=\t194620\t-290\tCACTCACCAGATTCAGCCCAGGACCAGAGGCTGCCGAGGGCAGGTGTGGGACGAAGTCAAGATGAAGTCAGTTCATTGTGTGGTTTTCGGTACCAGGCTAGACCTAGATTTGAACCCCAAGTCTGCTACTTAGATCATTCATTCAATGTGT\tFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFF:FFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tNM:i:0\tMD:Z:132\tMC:Z:151M\tAS:i:132\tXS:i:0\n+A00126:224:H7HMWDSX3:3:1101:9344:5306\t97\tTest_seq\t449503\t7\t60M\t=\t449503\t60\tGTTCGGACAGAACAAGGGGATACTGATTGGTTTAAAGTCAGGAAAGGTATGAGTCAGTGT\t,FFFF,FFF:FF,FF:FF:FF:F:,F::,FF:,FFFFFFFF::FF,,:FFF,FFF::,F,\tNM:i:4\tMD:Z:3T44G2C5G2\tMC:Z:60M\tAS:i:44\tXS:i:40\tXA:Z:Test_seq,+16926,60M,5;\n+A00126:224:H7HMWDSX3:3:1101:9344:5306\t145\tTest_seq\t449503\t12\t60M\t=\t449503\t-60\tGTTTGGACAGAACAAGGGGATACTGATTGGTTTAAAGTCAGGAAAGGTGTGCGCCAGGGT\tFFFFFFFFF:F::FF,FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFF:F:FFFF\tNM:i:1\tMD:Z:53T6\tMC:Z:60M\tAS:i:55\tXS:i:50\tXA:Z:Test_seq,-16926,60M,2;\n+A00126:224:H7HMWDSX3:3:1101:17607:5212\t81\tTest_seq\t83397\t60\t122S29M\t=\t93852\t10428\tGCAATGAAGCAGCAGTTTTTGTAGTGAAGGGAAATGTCCTGATAACATTAAGTAAGAAATGAACTACAGGCCAGGGCATTGGATTGATTTAGTGTGGAGTTTCTCCAGCAATTTGTCAGATCAATCCAGCTGATTTTTGTGTGTTTACCTT\t:FF:FFF:FFFF,FFFFFFFFFFFFFFFFF:FFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF\tNM:i:0\tMD:Z:29\tMC:Z:151M\tAS:i:29\tXS:i:0\tSA:Z:Test_seq,94155,-,122M29S,60,0;\n+A00126:224:H7HMWDSX3:3:1101:17607:5212\t2129\tTest_seq\t94155\t60\t122M29H\t=\t93852\t-425\tGCAATGAAGCAGCAGTTTTTGTAGTGAAGGGAAATGTCCTGATAACATTAAGTAAGAAATGAACTACAGGCCAGGGCATTGGATTGATTTAGTGTGGAGTTTCTCCAGCAATTTGTCAGATC\t:FF:FFF:FFFF,FFFFFFFFFFFFFFFFF:FFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tNM:i:0\tMD:Z:122\tMC:Z:151M\tAS:i:122\tXS:i:0\tSA:Z:Test_seq,83397,-,122S29M,60,0;\n+A0'..b'6:224:H7HMWDSX3:3:1116:31720:7545\t2129\tTest_seq\t303836\t60\t131M20H\t=\t303522\t-445\tATGAAACACTGCCCAGCCCTGCGCCATCCTCACAGTTGTTGTTATGCTTGAGCCCATTGTTGCAGCCACTGTGTCAATCCATGTTGGCCCTCTACTTTACCAAGCATGATGTCCTTCTCCAGGGAGTGATC\tFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:F,FFFFFFFFFFFFFFF:FFFFFF::F,FFFFFFFFF:F:FFFFF:FFF:FF:FFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tNM:i:0\tMD:Z:131\tMC:Z:151M\tAS:i:131\tXS:i:43\tSA:Z:Test_seq,305328,+,20M131S,6,0;\n+A00126:224:H7HMWDSX3:3:1116:31720:7545\t129\tTest_seq\t303522\t60\t151M\t=\t305328\t1807\tATCTTTTATTTGGGAGAAACAAGTCAGAATTAATTCCTGTTGATTGCACTGAATTATAAATGATGAAGAATCAGAAATCAGCTACTGGCCCACAGGCATGTTGCAGAAACTCAATAAATGTTAGCCATCATCTCCTTTTTCATCATCATAA\tFFFFFFF:FFFF:F:FFFFFFFFFF:FFF:FFFF:FFFF,FFFFFFFFF,FFFFF::FFF:FFFFFFFFFFFFFFF,F:FFFFFFFFFF:FF:FF:FFFF,FFF:FFF:FFFFFF:FFFFFF,F:F,FFFFF:FFF:FFF:FFFF,FFF:F\tNM:i:0\tMD:Z:151\tMC:Z:20M131S\tAS:i:151\tXS:i:0\n+A00126:224:H7HMWDSX3:3:1116:30870:8296\t97\tTest_seq\t169295\t60\t151M\t=\t169582\t438\tGTTTCCTTTCCTGTATTTCTTTAGTCAGTCTAGCCAATGGTTTATCAATTTTGTTAATTTTTTCAAAGAACCAGCTTTTGGCTTTGTTAATTCTTTCAATTGTTTTTCTGTTCTCTAATTCATTTAGTTCAGCTCTAATTTTTATTATTTG\tFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFF:FFFFFFF:FFF:F:FFFFFFFF:F:F:FFFFFFFFFFF:FFFFFFF,FFFFF:FFFF:F,FFFFFFFFFFFF\tNM:i:1\tMD:Z:14T136\tMC:Z:151M\tAS:i:146\tXS:i:107\n+A00126:224:H7HMWDSX3:3:1116:30870:8296\t145\tTest_seq\t169582\t60\t151M\t=\t169295\t-438\tGCTTTTGCTGTGTCCCAGAGGTTTTGATAGGAAGTATTTTCATTCTCGTTGCTTTCTATGAATTTCCTTATTCCCTCCTTGATGTCTTCTATAACCCAGTCTTTTTTCAGGAGGGTATTGTTCATTTTCCAAGTATTTGATTTCTTTTCCC\t:FFF:FFFFFFFFF,:FFF,FFFFF:FFFFFFF:FFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:\tNM:i:3\tMD:Z:46T11A22G69\tMC:Z:151M\tAS:i:136\tXS:i:22\n+A00126:224:H7HMWDSX3:3:1116:5186:8719\t81\tTest_seq\t169618\t60\t129M22S\t=\t169344\t-403\tTTTTCATTCTCGTTGCTTTCTATGAATTTCCTTATTCCCTCCTTGATGTCTTCTATAACCCAGTCTTTTTTCAGGAGGGTATTGTTCATTTTCCAAGTATTTGATTTCTTTTCCCTCGTTCTTCTGTTATTGATCGATCTGTCATACTCTG\tF:FFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFF:FFF:FFFFFFFFFFF\tNM:i:5\tMD:Z:10T11A22G70A3T8\tMC:Z:151M\tAS:i:104\tXS:i:0\n+A00126:224:H7HMWDSX3:3:1116:5186:8719\t161\tTest_seq\t169344\t60\t151M\t=\t169618\t403\tTTTGTTAATTTTTTCAAAGAACCAGCTTTTGGCTTTGTTAATTCTTTCAATTGTTTTTCTGTTCTCTAATTCATTTAGTTCAGCTCTAATTTTTATTATTTGTTTTCTTCTGGTGCCTGATGGATTCTTTTGTTGCTCACTTTCTATTTGT\tFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF,FFFFF:FFFF:FFFF,FF:FFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFF,FFFFFFFF,FFF:FFFFFF,FFFFFFFFFFFFF:FFFFFFF,FFFF,F:FFFFF,FFFF,F:F,\tNM:i:1\tMD:Z:123G27\tMC:Z:129M22S\tAS:i:146\tXS:i:101\n+A00126:224:H7HMWDSX3:3:1116:11080:9690\t97\tTest_seq\t171531\t60\t151M\t=\t171767\t387\tTTCCCTGGTCCTCCAGAAGTCCTAGTCTACATTCTAATTGCTCGAGTCTGCTCCTCTGACTTTCTATTGTGTTGTCAAATTCTATAATTTTATTGTTAATCTTTTGGATTTCTACATGCTGTCTCTCTATGTATTCTTGCAACTTATTAAT\tFFFFFFF:F,FFFFFFFFFF::FFFFFFFFFF:FFFFFFF:FF:F:F,FFFFFFFF:F:::,FFFF:FFFFFFFFFFF,FF:FFF:F,:FFFFFFF:,FFFFFFF::FFF:FF:F,:F,,F:::F,:FFFFF,FF,FFF,,F,:FFFFF:F\tNM:i:6\tMD:Z:22C29T16C6T6G47G19\tMC:Z:151M\tAS:i:121\tXS:i:53\n+A00126:224:H7HMWDSX3:3:1116:11080:9690\t145\tTest_seq\t171767\t60\t151M\t=\t171531\t-387\tATTTCATTTGTGATATCTTTAAGCATTCTGTAAATTAGTTTTTTATATTCTGTATCTGATAATTCCAGGATTGTATCTTCATTTGGGAAAGATTTTGATTCTTTTGTTTGGGGGGTTGGAGAAGCTGTCATGGTCTGTTTCTTTATGTGGT\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF,F:FFFFF::FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF\tNM:i:0\tMD:Z:151\tMC:Z:151M\tAS:i:151\tXS:i:0\n+A00126:224:H7HMWDSX3:3:1116:31367:10222\t97\tTest_seq\t168346\t60\t130M\t=\t168472\t256\tATCATGTCATCTGCAAATAGTGATAGCTTTACTTTGTCCTTACCAATCTGGATACCCTTTATTTTTTTGTCTAGCCTAATTGCCCTGGCTAGGACTTCAAGTACGATGTTGAATAAGAGTGGTGATAAAG\t*\tNM:i:7\tMD:Z:0G18A14C0C5G22C54C10\tMC:Z:130M\tAS:i:99\tXS:i:40\n+A00126:224:H7HMWDSX3:3:1116:31367:10222\t145\tTest_seq\t168472\t60\t130M\t=\t168346\t-256\tAAAGGGCATCCTTGTCTGGTTCCTGTTCTCAAGGGAAATGCTTTCAGGTTCTCTCCATTTAGAGTGATATTGGCTGTTGGCTTTGCATAGATGCCCTTTATTATGTTGAGGAATTTTCCTTCAATTCCTA\t*\tNM:i:0\tMD:Z:130\tMC:Z:130M\tAS:i:130\tXS:i:75\n' |