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Changeset 1:047a20d4258f (2021-04-02)

Previous changeset 0:79725ecf10a3 (2021-03-29)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 9f971aa7d32d756aa4763ab29d1770178a5ece6b"

modified:
clip_overlap.xml
macros.xml

added:
test-data/in1.sam
test-data/in2.sam
test-data/in3.sam

diff -r 79725ecf10a3 -r 047a20d4258f clip_overlap.xml
--- a/clip_overlap.xml Mon Mar 29 14:15:42 2021 +0000
+++ b/clip_overlap.xml Fri Apr 02 20:20:31 2021 +0000

@@ -1,4 +1,4 @@
-<tool id="bamutil_clip_overlap" name="BamUtil clipOverlap" version="@WRAPPER_VERSION@" profile="@PROFILE@">
+<tool id="bamutil_clip_overlap" name="BamUtil clipOverlap" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description></description>
     <macros>
         <import>macros.xml</import>

diff -r 79725ecf10a3 -r 047a20d4258f macros.xml
--- a/macros.xml Mon Mar 29 14:15:42 2021 +0000
+++ b/macros.xml Fri Apr 02 20:20:31 2021 +0000

@@ -1,5 +1,6 @@
<macros>
     <token name="@WRAPPER_VERSION@">1.0.15</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.09</token>
     <xml name="requirements">
         <requirements>

diff -r 79725ecf10a3 -r 047a20d4258f test-data/in1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in1.sam Fri Apr 02 20:20:31 2021 +0000

b'@@ -0,0 +1,103 @@\n+@HD\tVN:1.0\tSO:coordinate\n+@SQ\tSN:1\tLN:248956422\n+@SQ\tSN:2\tLN:242193529\n+@SQ\tSN:3\tLN:198295559\n+@SQ\tSN:4\tLN:190214555\n+@SQ\tSN:5\tLN:181538259\n+@SQ\tSN:6\tLN:170805979\n+@SQ\tSN:7\tLN:159345973\n+@SQ\tSN:8\tLN:145138636\n+@SQ\tSN:9\tLN:138394717\n+@SQ\tSN:10\tLN:133797422\n+@SQ\tSN:11\tLN:135086622\n+@SQ\tSN:12\tLN:133275309\n+@SQ\tSN:13\tLN:114364328\n+@SQ\tSN:14\tLN:107043718\n+@SQ\tSN:15\tLN:101991189\n+@SQ\tSN:16\tLN:90338345\n+@SQ\tSN:17\tLN:83257441\n+@SQ\tSN:18\tLN:80373285\n+@SQ\tSN:19\tLN:58617616\n+@SQ\tSN:20\tLN:64444167\n+@SQ\tSN:21\tLN:46709983\n+@SQ\tSN:22\tLN:50818468\n+@SQ\tSN:X\tLN:156040895\n+@SQ\tSN:Y\tLN:57227415\n+@SQ\tSN:MT\tLN:16569\n+@PG\tID:hisat2\tPN:hisat2\tVN:2.1.0\tCL:"/panfs/roc/galaxy/shared/miniconda3/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/risdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq"\n+@PG\tID:hisat2-55424A4\tPN:hisat2\tVN:2.1.0\tCL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq"\n+@PG\tID:hisat2-55424A4-3A2CCEF5\tPN:hisat2\tVN:2.1.0\tCL:"/panfs/roc/galaxy/shared/miniconda3/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/risdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq"\n+@PG\tID:samtools\tPN:samtools\tPP:hisat2-55424A4-3A2CCEF5\tVN:1.11\tCL:samtools sort -@ 1 -m 10240M -T sorttemp -O sam -o 0.sam /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075444.dat\n+@PG\tID:hisat2-3A2CCEF5\tPN:hisat2\tVN:2.1.0\tCL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq"\n+@PG\tID:samtools-6ADB4A65\tPN:samtools\tPP:hisat2-3A2CCEF5\tVN:1.11\tCL:samtools sort -@ 1 -m 10240M -T sorttemp -O sam -o 1.sam /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat\n+@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.11\tCL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075450.dat 0.sam 1.sam\n+@PG\tID:samtools.2\tPN:samtools\tPP:samtools-6ADB4A65\tVN:1.11\tCL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075450.dat 0.sam 1.sam\n+@PG\tID:hisat2-6ADB4A65\tPN:hisat2\tVN:2.1.0\tCL:"/panfs/roc/galaxy/shared/miniconda3/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/risdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile'..b'GTCAAGCTTCCAAGACTCCAGACACATCCAAATGAGG\tAE/EE/<EE//AEA<AEEEEEEEE6E/EEAEEEEAE6EE/EE///EE//EE<EEEAEAAEAAE/EEAEEEAAA6A\tAS:i:-3\tMD:Z:26G48\tNM:i:1\tNH:i:2\tXN:i:0\tXM:i:1\tZF:i:83\tZM:i:1\tZN:Z:6:52995709\tZI:i:-148\tZS:Z:CAAGCTCTCAAGGTCCATTTGTAGGATAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACACATCCAAATGAGG\tXO:i:0\tXG:i:0\tYS:i:-3\tYT:Z:CP\tZP:Z:6:52995848\tZC:Z:75M\tZQ:Z:AE/EE/<EE//AEA<AEEEEEEEE6E/EEAEEEEAE6EE/EE///EE//EE<EEEAEAAEAAE/EEAEEEAAA6A\tZT:Z:AS:i:-3;MD:Z:26G48;NM:i:1;NH:i:2;XN:i:0;XM:i:1;XO:i:0;XG:i:0;YS:i:-3;YT:Z:CP\n+NB500964:249:HHLFNBGX7:1:12312:5087:3846\t83\t6\t52995848\t60\t73M2S\t=\t52995649\t-274\tCAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACACATCCAAATGAAG\t<EEEEEEEEEEEEAEEEEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA\tAS:i:-2\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:73\tYS:i:0\tYT:Z:CP\tNH:i:1\n+NB500964:249:HHLFNBGX7:3:21607:1536:15142\t99\t6\t73518202\t60\t63M89N12M\t=\t73518250\t118\tGTGGCAATCCAATACAGGGGCATAGCCGGCGCTTATTTGGCCTGGATGGTTCAGGATAATCACCTGAGCAGTGAA\tAAAAAEEEEEEEEEEEAEEA/EEEEAEAEAEEEEEEEAEEE<EAA/EEEEE<EEAE/EA</A/AAAAAEAA/E/<\tAS:i:0\tZS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:75\tYS:i:-2\tYT:Z:CP\tXS:A:-\tNH:i:1\n+NB500964:249:HHLFNBGX7:3:21607:1536:15142\t147\t6\t73518250\t60\t2S15M89N58M\t=\t73518202\t-118\tTTGTTCAGGATAATCACCTGAGCAGTGAAGCCAGCTGCTTCCATTGGTGGGTCATTTTTGCTGTCACCAGCAACG\tA/<EAEEA//<//EA/AEAEE/EEA//EE<EEE/EEA/AEEEEEAAAEE/E/EEEEEEEEEEE/EEEEEEAAAAA\tAS:i:-2\tZS:i:-2\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:73\tYS:i:0\tYT:Z:CP\tXS:A:-\tNH:i:1\n+NB500964:249:HHLFNBGX7:2:21106:19199:5423\t99\t6\t73519036\t1\t75M\t=\t73519096\t135\tCCTTAACAATTTCCTCATATCTCTTCTGGCTGTAGGGTGGCTCAGTGGAATCCATTTTGTTAACACCGACAATTA\tAAAAAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\tAS:i:0\tZS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:75\tYS:i:0\tYT:Z:CP\tNH:i:3\n+NB500964:249:HHLFNBGX7:2:21106:19199:5423\t147\t6\t73519096\t1\t75M\t=\t73519036\t-135\tTAACACCGACAATTAGTTGTTTCACACCCAGTGTGTAAGCCAGAAGGGCATGCTCTCGGGTCTGCCCATTCTTGG\tEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEAAAAA\tAS:i:0\tZS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:75\tYS:i:0\tYT:Z:CP\tNH:i:3\n+NB500964:249:HHLFNBGX7:1:23112:23126:11688\t355\t6\t73519370\t1\t75M\t=\t73519434\t139\tGTCTCTGTGTCCTGGGGCATCAATGATAGTCACATAGTACTTGCTGGTCTCAAATTTCCACAAGGAGATATCAAT\tAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEE\tAS:i:0\tZS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:75\tYS:i:0\tYT:Z:CP\tNH:i:2\n+NB500964:249:HHLFNBGX7:1:23112:23126:11688\t403\t6\t73519434\t1\t75M\t=\t73519370\t-139\tGAGATATCAATGGTGATACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCC\tEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEEEEEEEEAAAAA\tAS:i:0\tZS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:75\tYS:i:0\tYT:Z:CP\tNH:i:2\n+NB500964:249:HHLFNBGX7:4:13509:13430:12762\t355\t6\t73519451\t1\t66M366N9M\t=\t73519983\t241\tACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCCTTTCCCATCTCAGCAGC\tAAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEE/EE/EEEEEAEEAEEEAAEEEEEEEE<E<\tAS:i:0\tMD:Z:75\tNM:i:0\tNH:i:3\tXN:i:0\tXM:i:0\tZS:i:0\tXO:i:0\tXG:i:0\tYS:i:0\tYT:Z:CP\tXS:A:-\n+NB500964:249:HHLFNBGX7:4:13509:13430:12762\t355\t6\t73519451\t1\t66M366N9M\t=\t73519983\t241\tACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCCTTTCCCATCTCAGCAGC\tAAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEE/EE/EEEEEAEEAEEEAAEEEEEEEE<E<\tAS:i:0\tMD:Z:75\tNM:i:0\tNH:i:3\tXN:i:0\tXM:i:0\tZS:i:0\tXO:i:0\tXG:i:0\tYS:i:0\tYT:Z:CP\tXS:A:-\n+NB500964:249:HHLFNBGX7:4:13509:13430:12762\t355\t6\t73519451\t1\t66M366N9M\t=\t73519983\t241\tACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCCTTTCCCATCTCAGCAGC\tAAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEE/EE/EEEEEAEEAEEEAAEEEEEEEE<E<\tAS:i:0\tMD:Z:75\tNM:i:0\tNH:i:3\tXN:i:0\tXM:i:0\tZP:Z:6:73519451\tZC:Z:66M366N9M\tZF:i:99\tZM:i:1\tZN:Z:6:73519983\tZS:i:0\tXO:i:0\tXG:i:0\tYS:i:0\tYT:Z:CP\tXS:A:-\tZI:i:241\tZS:Z:ACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCCTTTCCCATCTCAGCAGC\tZQ:Z:AAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEE/EE/EEEEEAEEAEEEAAEEEEEEEE<E<\tZT:Z:AS:i:0;MD:Z:75;NM:i:0;NH:i:3;XN:i:0;XM:i:0;ZS:i:0;XO:i:0;XG:i:0;YS:i:0;YT:Z:CP;XS:A:-\n'

diff -r 79725ecf10a3 -r 047a20d4258f test-data/in2.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in2.sam Fri Apr 02 20:20:31 2021 +0000

b'@@ -0,0 +1,96 @@\n+@HD\tVN:1.0\tSO:coordinate\n+@SQ\tSN:1\tLN:248956422\n+@SQ\tSN:2\tLN:242193529\n+@SQ\tSN:3\tLN:198295559\n+@SQ\tSN:4\tLN:190214555\n+@SQ\tSN:5\tLN:181538259\n+@SQ\tSN:6\tLN:170805979\n+@SQ\tSN:7\tLN:159345973\n+@SQ\tSN:8\tLN:145138636\n+@SQ\tSN:9\tLN:138394717\n+@SQ\tSN:10\tLN:133797422\n+@SQ\tSN:11\tLN:135086622\n+@SQ\tSN:12\tLN:133275309\n+@SQ\tSN:13\tLN:114364328\n+@SQ\tSN:14\tLN:107043718\n+@SQ\tSN:15\tLN:101991189\n+@SQ\tSN:16\tLN:90338345\n+@SQ\tSN:17\tLN:83257441\n+@SQ\tSN:18\tLN:80373285\n+@SQ\tSN:19\tLN:58617616\n+@SQ\tSN:20\tLN:64444167\n+@SQ\tSN:21\tLN:46709983\n+@SQ\tSN:22\tLN:50818468\n+@SQ\tSN:X\tLN:156040895\n+@SQ\tSN:Y\tLN:57227415\n+@SQ\tSN:MT\tLN:16569\n+@PG\tID:hisat2\tPN:hisat2\tVN:2.1.0\tCL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq"\n+@PG\tID:hisat2-55424A4\tPN:hisat2\tVN:2.1.0\tCL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq"\n+@PG\tID:hisat2-55424A4-3A2CCEF5\tPN:hisat2\tVN:2.1.0\tCL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq"\n+@PG\tID:samtools\tPN:samtools\tPP:hisat2-55424A4-3A2CCEF5\tVN:1.11\tCL:samtools sort -@ 1 -m 10240M -T sorttemp -O sam -o 0.sam /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075445.dat\n+@PG\tID:hisat2-3A2CCEF5\tPN:hisat2\tVN:2.1.0\tCL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq"\n+@PG\tID:samtools-6ADB4A65\tPN:samtools\tPP:hisat2-3A2CCEF5\tVN:1.11\tCL:samtools sort -@ 1 -m 10240M -T sorttemp -O sam -o 1.sam /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat\n+@PG\tID:samtools.1\tPN:samtools\tPP:samtools\tVN:1.11\tCL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075449.dat 0.sam 1.sam\n+@PG\tID:samtools.2\tPN:samtools\tPP:samtools-6ADB4A65\tVN:1.11\tCL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075449.dat 0.sam 1.sam\n+@PG\tID:hisat2-6ADB4A65\tPN:hisat2\tVN:2.1.0\tCL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites'..b'CCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGAC\tEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6AAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:75\tYS:i:0\tYT:Z:CP\tNH:i:1\n+NB500964:249:HHLFNBGX7:3:21512:8039:1524\t83\t6\t52995836\t60\t75M\t=\t52995730\t-181\tAGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACAC\t/EA/EEEEAE/E/A</E/E/6/EEEEEEEE/EEEEE/EEEEEAEEEEEEEE6EEEEAE6EEEEEEEEEEEAAAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:75\tYS:i:0\tYT:Z:CP\tNH:i:1\n+NB500964:249:HHLFNBGX7:3:22611:13268:8039\t83\t6\t52995848\t1\t75M\t=\t52995709\t-148\tCAAGCTCTCAAGGTCCATTTGTAGGATAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACACATCCAAATGAGG\tAE/EE/<EE//AEA<AEEEEEEEE6E/EEAEEEEAE6EE/EE///EE//EE<EEEAEAAEAAE/EEAEEEAAA6A\tAS:i:-3\tMD:Z:26G48\tNM:i:1\tNH:i:2\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tYS:i:-3\tYT:Z:CP\n+NB500964:249:HHLFNBGX7:3:22611:13268:8039\t339\t6\t52995848\t1\t75M\t=\t52995709\t-140\tCAAGCTCTCAAGGTCCATTTGTAGGATAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACACATCCAAATGAGG\tAE/EE/<EE//AEA<AEEEEEEEE6E/EEAEEEEAE6EE/EE///EE//EE<EEEAEAAEAAE/EEAEEEAAA6A\tAS:i:-3\tMD:Z:26G48\tNM:i:1\tNH:i:2\tXN:i:0\tXM:i:1\tZF:i:83\tZM:i:1\tZN:Z:6:52995709\tZI:i:-148\tZS:Z:CAAGCTCTCAAGGTCCATTTGTAGGATAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACACATCCAAATGAGG\tXO:i:0\tXG:i:0\tYS:i:-3\tYT:Z:CP\tZP:Z:6:52995848\tZC:Z:75M\tZQ:Z:AE/EE/<EE//AEA<AEEEEEEEE6E/EEAEEEEAE6EE/EE///EE//EE<EEEAEAAEAAE/EEAEEEAAA6A\tZT:Z:AS:i:-3;MD:Z:26G48;NM:i:1;NH:i:2;XN:i:0;XM:i:1;XO:i:0;XG:i:0;YS:i:-3;YT:Z:CP\n+NB500964:249:HHLFNBGX7:3:13604:19654:15542\t99\t6\t53004731\t60\t75M\t=\t53004936\t280\tCTTAAATTGCACCCCTGTTGCAATACTGCATTAATATTATTACATTTTTCAAAATCTGTAGAAAATATTATCTGG\tAAAAAEEEEEEEA//EEEEEEEEEEEEEEAEEEEEEEEEEEEAEE/EEEEEEEEEEEEEEEEE/EEEEEEE/EEE\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:75\tYS:i:0\tYT:Z:CP\tNH:i:1\n+NB500964:249:HHLFNBGX7:3:13604:19654:15542\t147\t6\t53004936\t60\t75M\t=\t53004731\t-280\tAATAATTTTATACAAAAAAGCCTACTGCATTCAAATCAATATTTTAAAAAAAAACTTTAAAAAAGAATATTGACA\tEEEEEAEEEEEEEEEEEEEAEE/EAEEEEEEEEEEEEEEEEEEEEEEEEEEAEAAEEAEEEEAAEEEEEEAAAAA\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:75\tYS:i:0\tYT:Z:CP\tNH:i:1\n+NB500964:249:HHLFNBGX7:4:13509:13430:12762\t99\t6\t73519451\t1\t66M366N9M\t=\t73519983\t241\tACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCCTTTCCCATCTCAGCAGC\tAAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEE/EE/EEEEEAEEAEEEAAEEEEEEEE<E<\tAS:i:0\tMD:Z:75\tNM:i:0\tNH:i:3\tXN:i:0\tXM:i:0\tZS:i:0\tXO:i:0\tXG:i:0\tYS:i:0\tYT:Z:CP\tXS:A:-\n+NB500964:249:HHLFNBGX7:4:13509:13430:12762\t355\t6\t73519451\t1\t66M366N9M\t=\t73519983\t241\tACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCCTTTCCCATCTCAGCAGC\tAAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEE/EE/EEEEEAEEAEEEAAEEEEEEEE<E<\tAS:i:0\tMD:Z:75\tNM:i:0\tNH:i:3\tXN:i:0\tXM:i:0\tZS:i:0\tXO:i:0\tXG:i:0\tYS:i:0\tYT:Z:CP\tXS:A:-\n+NB500964:249:HHLFNBGX7:4:13509:13430:12762\t355\t6\t73519451\t1\t66M366N9M\t=\t73519983\t241\tACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCCTTTCCCATCTCAGCAGC\tAAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEE/EE/EEEEEAEEAEEEAAEEEEEEEE<E<\tAS:i:0\tMD:Z:75\tNM:i:0\tNH:i:3\tXN:i:0\tXM:i:0\tZP:Z:6:73519451\tZC:Z:66M366N9M\tZF:i:99\tZM:i:1\tZN:Z:6:73519983\tZS:i:0\tXO:i:0\tXG:i:0\tYS:i:0\tYT:Z:CP\tXS:A:-\tZI:i:241\tZS:Z:ACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCCTTTCCCATCTCAGCAGC\tZQ:Z:AAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEE/EE/EEEEEAEEAEEEAAEEEEEEEE<E<\tZT:Z:AS:i:0;MD:Z:75;NM:i:0;NH:i:3;XN:i:0;XM:i:0;ZS:i:0;XO:i:0;XG:i:0;YS:i:0;YT:Z:CP;XS:A:-\n+NB500964:249:HHLFNBGX7:3:12402:8344:2452\t99\t6\t73519463\t60\t54M366N21M\t=\t73519916\t162\tCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCCTTTCGCATCTCAGCAGCCTCCTTCTCAAA\tA6AAAEE6EEE6/EEEE/<EEEE/<EEEEEEEEEEEE//EEE/E<E/////<E/A/AA///AAEEE<//E</</A\tAS:i:-3\tZS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:50C24\tYS:i:-9\tYT:Z:CP\tXS:A:-\tNH:i:1\n+NB500964:249:HHLFNBGX7:3:12402:8344:2452\t147\t6\t73519916\t60\t75M\t=\t73519463\t-162\tTCTTTTGGCGATGCCACCGCATTTATAGATCAGATGGCCAGTAGTGGTGGACTTGCCCGAAGCTACGGGTCCAAT\t/EEAE6</EE//EEE//AEEEA/EE/<//AE/EE/E//AEAA/EAAAA/AE6EE///E//A/EAE6E/EE/AAAA\tAS:i:-9\tZS:i:-9\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:7T53T5T7\tYS:i:-3\tYT:Z:CP\tNH:i:1\n'

diff -r 79725ecf10a3 -r 047a20d4258f test-data/in3.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in3.sam Fri Apr 02 20:20:31 2021 +0000