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Changeset 26:9ffcddf6f9c0 (2020-02-17)

Previous changeset 25:7d34178f2812 (2019-06-11) Next changeset 27:a1f0b3f4b781 (2020-02-19)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit cbe534af56ee782e8d1aa0fa872059d2a5e42db8"

modified:
picard_SamToFastq.xml

added:
test-data/picard_SamToFastq_1.fq
test-data/picard_SamToFastq_2.fq
test-data/picard_SamToFastq_se.bam
test-data/picard_SamToFastq_se.fq
test-data/picard_SamToFastq_u.fq

diff -r 7d34178f2812 -r 9ffcddf6f9c0 picard_SamToFastq.xml
--- a/picard_SamToFastq.xml Tue Jun 11 02:36:54 2019 -0400
+++ b/picard_SamToFastq.xml Mon Feb 17 10:24:29 2020 -0500

[

b'@@ -2,13 +2,11 @@\n <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description>\n <macros>\n <import>picard_macros.xml</import>\n- <token name="@WRAPPER_VERSION@">1</token>\n+ <token name="@WRAPPER_VERSION@">2</token>\n </macros>\n <expand macro="requirements" />\n <command detect_errors="exit_code"><![CDATA[\n \n- echo "BAM" > $report && ## This is necessary for output dataset detection (see output tags below)\n-\n @java_options@\n @symlink_element_identifier@\n \n@@ -17,22 +15,26 @@\n \n INPUT=\'$escaped_element_identifier\'\n \n- #if str( $output_per_rg ) == "true":\n- OUTPUT_PER_RG=true\n- OUTPUT_DIR=.\n- #elif str( $output_per_rg ) == "false" and str( $interleave ) == "false":\n- FASTQ=READ1.fastq\n- SECOND_END_FASTQ=READ2.fastq\n- UNPAIRED_FASTQ=UNPAIRED_READS.fastq\n- #elif str( $output_per_rg ) == "false" and str( $interleave ) == "true":\n- FASTQ=INTERLEAVED.fastq\n+ #if str($single_or_paired) == "pe_interleaved":\n+ FASTQ=\'${interleaved_fastq}\'\n+ INTERLEAVE=TRUE\n+ #else if str($single_or_paired) == "pe_sep":\n+ F=\'${fq1}\'\n+ F2=\'${fq2}\'\n+ FU=\'${fq_u}\'\n+ #else\n+ F=\'${fq_single}\'\n #end if\n \n RE_REVERSE="${re_reverse}"\n- INTERLEAVE="${interleave}"\n+\n INCLUDE_NON_PF_READS="${include_non_pf_reads}"\n- CLIPPING_ATTRIBUTE="${clipping_attribute}"\n- CLIPPING_ACTION="${clipping_action}"\n+ #if len(str($clipping_attribute)) > 0:\n+ CLIPPING_ATTRIBUTE="${clipping_attribute}"\n+ #end if\n+ #if len(str($clipping_action)) > 0:\n+ CLIPPING_ACTION="${clipping_action}"\n+ #end if\n READ1_TRIM="${read1_trim}"\n \n #if int($read1_max_bases_to_write) > -1:\n@@ -47,7 +49,6 @@\n \n INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"\n \n-\n VALIDATION_STRINGENCY="${validation_stringency}"\n QUIET=true\n VERBOSITY=ERROR\n@@ -57,12 +58,16 @@\n <inputs>\n \n <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>\n- <param name="output_per_rg" type="boolean" checked="False" label="Do you want to output a fastq file per read group (two fastq files per read group if the group is paired)" help="OUTPUT_PER_RG; default=False"/>\n+ <param name="single_or_paired" type="select" label="Output format">\n+ <option value="se" >Single-end</option>\n+ <option value="pe_interleaved" selected="true">Paired-end (one interleaved output file)</option>\n+ <option value="pe_sep">Paired-end (two separate output files)</option>\n+ </param>\n+\n <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/>\n- <param name="interleave" type="boolean" label="Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe which end it came from" help="INTERLEAVE; default=False"/>\n <param name="include_non_pf_reads" type="boolean" label="Include non-PF reads from the SAM/BAM dataset into the output FASTQ" help="INCLUDE_NON_PF_READS; PF means \'passes filtering\'. Reads whose \'not passing quality controls\' flag is set are non-PF reads; default=False"/>\n- <param name="clipping_attribute" type="text" value="null" label="The attribute that stores the position at which the SAM/BAM record should be clipped" help="CLIPPING_ATTRIBUTE; default=null"/>\n- <param name="clipping_action" type="text" value="null" label="The action that should be taken with clipped reads: \'X\' means the reads and qualities should be trimmed at the clipped position; \'N\' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region" help="CLIPPING_ACTION; default=null"/>\n+ <param name="clipping_attribute" type="text" value="" label'..b' pattern="(?P<designation>.+)\\.fastq" ext="fastqsanger" visible="true"/>\n+ <data format="fastqsanger" name="fq_single" label="${tool.name} on ${on_string}: reads as fastq">\n+ <filter>output_type[\'single_or_paired\'] == \'se\'</filter>\n+ </data>\n+\n+ <data format="fastqsanger" name="interleaved_fastq" label="Interleaved pairs from ${tool.name} on ${on_string}">\n+ <filter>output_type[\'single_or_paired\'] == \'pe_interleaved\'</filter>\n+ </data>\n+\n+ <data format="fastqsanger" name="fq1" label="Paired-end forward strand from ${tool.name} on ${on_string}">\n+ <filter>output_type[\'single_or_paired\'] == \'pe_sep\'</filter>\n+ </data>\n+\n+ <data format="fastqsanger" name="fq2" label="Paired-end reverse strand from ${tool.name} on ${on_string}">\n+ <filter>output_type[\'single_or_paired\'] == \'pe_sep\'</filter>\n+ </data>\n+\n+ <data format="fastqsanger" name="fq_u" label="Paired-end unpaired reads from ${tool.name} on ${on_string}">\n+ <filter>output_type[\'single_or_paired\'] == \'pe_sep\'</filter>\n </data>\n </outputs>\n \n <tests>\n <test>\n <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>\n+ <param name="single_or_paired" value="pe_interleaved" />\n <param name="output_per_rg" value="false"/>\n <param name="re_reverse" value="true"/>\n- <param name="interleave" value="true"/>\n <param name="include_non_pf_reads" value="false"/>\n- <param name="clipping_attribute" value="null" />\n- <param name="clipping_action" value="null" />\n+ <param name="clipping_attribute" value="" />\n+ <param name="clipping_action" value="" />\n <param name="read1_trim" value="0" />\n <param name="read1_max_bases_to_write" value="-1"/>\n <param name="read2_trim" value="0" />\n <param name="read2_max_bases_to_write" value="-1"/>\n <param name="include_non_primary_alignments" value="false"/>\n- <output name="report">\n- <assert_contents>\n- <has_line line="BAM" />\n- </assert_contents>\n- <discovered_dataset designation="INTERLEAVED" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>\n- </output>\n+ <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>\n+ </test>\n+ <test>\n+ <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>\n+ <param name="single_or_paired" value="pe_sep" />\n+ <param name="output_per_rg" value="false"/>\n+ <param name="re_reverse" value="true"/>\n+ <param name="include_non_pf_reads" value="false"/>\n+ <param name="clipping_attribute" value="" />\n+ <param name="clipping_action" value="" />\n+ <param name="read1_trim" value="0" />\n+ <param name="read1_max_bases_to_write" value="-1"/>\n+ <param name="read2_trim" value="0" />\n+ <param name="read2_max_bases_to_write" value="-1"/>\n+ <param name="include_non_primary_alignments" value="false"/>\n+ <output name="fq1" file="picard_SamToFastq_1.fq" ftype="fastqsanger"/>\n+ <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/>\n+ <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/>\n+ </test>\n+ <test>\n+ <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>\n+ <param name="single_or_paired" value="se" />\n+ <param name="output_per_rg" value="false"/>\n+ <param name="re_reverse" value="true"/>\n+ <param name="include_non_pf_reads" value="false"/>\n+ <param name="clipping_attribute" value="" />\n+ <param name="clipping_action" value="" />\n+ <param name="read1_trim" value="0" />\n+ <param name="read1_max_bases_to_write" value="-1"/>\n+ <param name="read2_trim" value="0" />\n+ <param name="read2_max_bases_to_write" value="-1"/>\n+ <param name="include_non_primary_alignments" value="false"/>\n+ <output name="fq_single" file="picard_SamToFastq_se.fq" ftype="fastqsanger"/>\n </test>\n </tests>\n \n'

diff -r 7d34178f2812 -r 9ffcddf6f9c0 test-data/picard_SamToFastq_1.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_SamToFastq_1.fq Mon Feb 17 10:24:29 2020 -0500

b'@@ -0,0 +1,4000 @@\n+@M01368:28:000000000-A5KYY:1:1101:10045:12104/1\n+ATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGG\n++\n+?????B/B-<5BBA<B/+,6>@AEHFF>CFBA>EC=C>>CED?CFCEDA-AC/AE=ACE,CCCDHHHH-5C5EG>><<EHGHCEDE+?7<CCD?D@DF?:DAE=EDEDDDD;@<BBEE@2.?8:::?EEEEEEA::*?A:88//?A20?8A0/8:AEEEEC:A*00?:?E?CE:/:/?::C??AC?**:0:*??CEA?EE?*8?8CE8A*888A*??://?AEEAAACAE\n+@M01368:28:000000000-A5KYY:1:1101:10126:23848/1\n+CTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCG\n++\n+??AAABAADDDDDDDEGGGGGGIIIHIHIHHEEHHIIIIIEGHHIIIHGHIIHHHHHIIIIGFHHIIIIIIIHHHHHHHHHHHHHHHHHHHFHHHGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGCGGGG<CGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGCGG\n+@M01368:28:000000000-A5KYY:1:1101:10229:22034/1\n+CACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAA\n++\n+?????BBBDDDDEDDDGGFGGGHHHHHHIIHFHHFFHIICGGHHIIIIIIIIIHIIHHHFHHHHHHEEDFIIIIIIHIIIGIIIDHHHIIHHIHHHHHHHGDGCEGGGGGGGGGGGGGGGGGGGGGGGCC>EGGGGGGGGGGGGGGEGGGGGGGCGGGGGGGGGGGGGGGEEEEGGEGGGGGGGGGGGGGGGCE?>GGGGGCEEEEGGGGGGEEGGGGGGGEEGGGGGGGGGGEGEEEEEECGGG\n+@M01368:28:000000000-A5KYY:1:1101:10278:20774/1\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTA\n++\n+?????BBBDDDDDDDDGGGGGGHFFHHIICGHIFEFFECFFHHHHHHIHIIIHIIIHHIHHHHE@FHIIIGIIIIIFHIHHHHHHHHHFHHHDFHFHGHHHHEHHHHGGGGGGGGGGEEGGGGGGG@EGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGEEGGGGGGGGGCCEECEE:CEGGGGGGGGEGGGGGGEGGGGGGGGCEEEGEGGEEGGGGGEGEGGEGGGEGC80?EEEGGG?CEGEEGGGE\n+@M01368:28:000000000-A5KYY:1:1101:10291:14859/1\n+GTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTT\n++\n+<????BBBDDDDDDDDFFFFFFIFHIIIHIIIIFGHGHAEHHHIIHHHHIHHIHHIIFGHHI7EFHGFGHEFHHHGIHHHHHHIHHIHHEHHHFIIIHGGHHHHHHHHHHHHHHHHHFFFDFEFFFEEEEEFFFFEEEEFFFEEEFFFFFFEEDDDEFFFFFFFEEDEFFDDDE?FFFFFEEFFFFFFFFFFEFFEFFD888A?CF?EEFFEEFFCEEFFFFEFEEEFEFEFFEEEEE??EEFEEFFEF\n+@M01368:28:000000000-A5KYY:1:1101:10479:22035/1\n+ATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATT\n++\n+?????BBBDDDDDDD<FFFFFFHHFFEHHHHFGHGGHGGFHHHHHHHFGHHHHHHHHGHHHHHFGHGHHHHHHHHFHGGFHHFFHHHHHHHHHHHHHHHHH@FHHHHHHFFEFFFFEDDEFFFEEEEEFFFFEEE@;EFFFFECEDDDEFEDDDEDFFFFEEEFFFFFEFFEAAFEFAED?EFEAAEEAEEEFFFF:8AEFCCEECEEFFEEEEE?EEAE??CCECEEEAEFFFF?EEC?8C*8AEF???E\n+@M01368:28:000000000-A5KYY:1:1101:10581:22138/1\n+CTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTA\n++\n+??????A@DDDDDDDDGFGGFFHIHHHHIHHHHHIIIIAFGHHIHIIIIIIIHHHIHHHGHIIIIIHHHIIIIGHHHFFHIIIHHHFFHHHHHHHHHHHHHHHHGHGGFGGGFGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGG8CEGGGGGGGGGGGGGGDEGGGGEGGGGGGGGGGGGGGGGGGE<CEDEGGGGGDGGGGGGGGGGEGGGGG8C\n+@M01368:28:000000000-A5KYY:1:1101:10696:7547/1\n+AAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCA'..b'AAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGG\n++\n+???AABBBDDDDDDDDGGGGGGHIIIIHHHHIIIIIIIIHIIIIHIIHCFHHFHHHIIIIIIIIHHEHIIIHHHHIIIIIHHFHIIIIHIIHIHHHHHHHHHFHHHHHHHGGGGGGGGGGGGGGGGGGGGGGGGGGBDGGGGGGGGGGGGGGGGGGGEEGGGGGGGGGGGGGGGGGGGGGGGGCEEEGEGEGGGGGGGEGGGGGGGGGEGGGGGGGGGGGGGGGGGGGEGGG?EGGGGGEGGGCEEC\n+@M01368:28:000000000-A5KYY:1:1106:19331:13430/1\n+GTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCC\n++\n+????A7?BDDDDDDDDGGGGGGIIHEHHHAEHHHIHHIIIIIIIIIIHHIIIHHHHIIIIIIIIIGHHIIIIIHHHHHHIHII8EEGHHHHHDHHHHHHHHGGGGGGGGGGGGGGGGGGGHGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGCCEEGGGGGG?CGEGGGGGGGGCCGGGGGGGGGGGGGGG\n+@M01368:28:000000000-A5KYY:1:1106:19484:14339/1\n+CTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATATTAC\n++\n+????AB?BDDDDDDDDFFFFFFIIHHHHIIHHHHHIIIIIIHIIIIIIIIHIIIIHEIIHFGHHHHIIEHGHIIIIIIIDGHHIIIIIIHIIIHHHHHHHHHHHHHHFHHHHHCFFFFFFFFEFFFFEED<AFFFFFFDEDDEEFFFEFFEDDDEADEEDFFFEDDDDDFEFEFFFFFFFFDEEFFFFFFFFFFFFEEFEEFEFFFEFFEEEFFEFFFFFFEEEDDFFFEFEFFEEAEEEC\n+@M01368:28:000000000-A5KYY:1:1106:19767:21874/1\n+AGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTAT\n++\n+??????BBDDDDDDDDGGGGGGHHHIIIIHHIIHIIIIHIIIHHHHIIIIIIIHHHIHHFHIIIHHHH@FHHIIIIIIIIIIHHIIIIIHHHHHEHHFHHHHHFFHHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGGGGGGGGG<CEGGGGE<)8CCCGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGD>AGGGGGGGEGGCEG>G8CCEEGGGGGGGGGGGEEGGGGEGEGGGGGGCG\n+@M01368:28:000000000-A5KYY:1:1106:20079:20293/1\n+TCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATACCATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGT\n++\n+AAAA????DDDDBDDDGCFGGGIIIIIIIIIIIHIIIIIIIIHHHHHHIIIIFGHHIIIIIICGHHIIFHEHFHIIHHG?EGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGAGGGGGGGGGGGGGGGGGEGGGGGEGGGGGGGG?CEGGGGGGE*:CGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC\n+@M01368:28:000000000-A5KYY:1:1106:20084:8979/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATATT\n++\n+????5.<?BDDDDDDDF?FFEEHHEHFCHHGF?CFHGFFFHHDHCAEFHHHHHHHCDFGHHFHHFFHHHHHHHFFFHHHFFGHDGBEGHHCEFGHDGHFHHFHHHDHHHHHHHHHFFFFFFFFFBADEFEEFEEEFFCC@6>DEEFFFFF>DDDA.?*ACEFED>>EE8?E8C8AA82;>DEFFEFEEAEFFF>E):AEEFEFFFFFEEEFEFE?EECEFAA?CEEFFFFFEF?AE8DFAC??:CEEFFFF\n+@M01368:28:000000000-A5KYY:1:1106:20271:14486/1\n+GGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCC\n++\n+???????BBDDDD<?DFGGGGGHIIHHHHHIIIIIHHIIIIHIFHHIIHHHIIIIIIIIIIIHFEHHHIIHHDHIIHHHHHIIIIIIIIIHHHIIHHHHHHHHHHHHHCFFHHHHHHHHGGGGGGGGGGGGGGEBGGGGGGGGGGGGGGEGGGECEGEGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG<EGGGGDGGGGGGGGGGGGGGGGGEEECAEEGGGGGGGGGGGGGGGCECEGGGGGGG\n+@M01368:28:000000000-A5KYY:1:1106:20363:9345/1\n+TCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACG\n++\n+?<????BBDBBDDBDBFCFFFFHHHHHHHFFGHDFEHHEHHHHHHHHFHHHHHHHHFHHHHHHHEHFHHHHHHEFGFHHHHHHFFHHF=EHHHHHHHHEDEEHHHHHHFFFFHHHFFFAFFFFFFEFEEDBEE@D4AECEFFED>>DAEEEFCAEE;88AEDEEDFFFE?DDDDEFFEFFFE?AAEDE?AC*A?ECEEEEEFFEEF:EEEFEFFFFFFFAEEEFFFEEEDDFACA\n'

diff -r 7d34178f2812 -r 9ffcddf6f9c0 test-data/picard_SamToFastq_2.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_SamToFastq_2.fq Mon Feb 17 10:24:29 2020 -0500

b"@@ -0,0 +1,4000 @@\n+@M01368:28:000000000-A5KYY:1:1101:10045:12104/2\n+CCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATAT\n++\n+?????<<<B<BBBBB<>CFFFFHEHHH?-CEFFB?ECC??EFFDDGDEHFFDD?A?C??;5AEAEGCFFDFBEDC-AFHHFFFHHD*<DDDCGHHHHHFHFFF@@+77D@=DEFHFFBBA=8.?CEECC????8EEEEECC?.8??AA;A?'8??E;;'82AC*8AECCEEEE2AEEE?EE:?AC::AE?AEE::*0:C?A?EC?C*:?E:/?A?848:?CECEEEEECE\n+@M01368:28:000000000-A5KYY:1:1101:10126:23848/2\n+GTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCCCTGAAGTAGGAACCAG\n++\n+?????BBBDDDEDDDDGCFFDEHHHIIIIIIIIHGHFHHIHHHEHIHHHHHHFHIIIIHIIHHHHEDFHIGBCEHHHHHHHEHHHHHDHHHHGHEEHHHG?DEGG:BGGGGGCCEBEEGEGBD>EGGGGGEGGGGGGGGGGGGGGCG?CD0?CECCEC8CEGGCEE*8?CEECCEEGCGGGGGGEEECGGEEGECCCE:CCGECCA8)?CCE:CEGGCEGGC?CEE?EEGGGGC*8*9C*?EGG?*:9)?8\n+@M01368:28:000000000-A5KYY:1:1101:10229:22034/2\n+TTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTG\n++\n+?A???BBBDDDDDDDDGFFFFGFFHHHHHHHHHIIIIIHIIGHHIIDDHH9DECEFEHHIIIIIIIFFEGGFDEHHHHHHHHIIHHHHFFGIIHHHDHHHHHHH-DDFFHEEGEGFEDDB=DDECGGEEGGEGEGGGG<<EGGEEEEE>>>EGGGGGG8EC?CGGEGGGEGGGGGGGEEEEGACC?C1:8*0*CCGGGG:??CEGGCEEE:CEGGECCECECC*:::?CC?CG:C:CCAECCEC8\n+@M01368:28:000000000-A5KYY:1:1101:10278:20774/2\n+CATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATAT\n++\n+<<???BBBDDDDDDDBFFF??EHEHFHHHHHHHHHHHHHHHHHHHBHHHHHFHHHBAFHGBFHHFHHHDHHHHFHFFHHHFHHHDFGEHHHHFHHHHHDGHFHHHHD)CEHDFFHFFFFFFFFFFF@BEEEEEEDDEEEE@E;?EEEEEEEDD8>AAEEECEEEDDDA?;EEDEECA?DD;>CCEEEE:C?:ACDEEEEECEEE:AAEEE?:?EEEEEEECEEEEECEEEEEEEEEEDDECCAE?CEA?CE\n+@M01368:28:000000000-A5KYY:1:1101:10291:14859/2\n+AAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGAC\n++\n+?????BBBDDDDDDDDFFEFFFFHIIHHHHIIIIIIIIIIIIHIHIHHHHHHHDHCHHIIIIHHIIHHIHHHFDGHHHHHFHIIEDEHDDEFFFFFFDDDDEEFEFFFFED>;EEDEEDFFFEDDDDDEECEEFFFEFFFDEEEFEFFFFAEFFFFFF?EFFEFEEEEEEF?CAEFEFFFFE?>>EFFEEFFF??AEEEEEECED8>DDFFFFFFFFEEEA::0:ACEEEFFFFF?EF*?EEEFCECEE\n+@M01368:28:000000000-A5KYY:1:1101:10479:22035/2\n+GACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAAT\n++\n+?????BBBDDDBBBDDFFFFFFIHHHIHFHHHHIIIIIIIFIIIIHHHFHHIGHHIHGFHHHIGHHIIHHEHIHHHIFHHHHHHHIIIHHIHFDHIIHIGHFFHFHHHHHEHEHHFFDFFFFFFFFFFDEFFFFFEFEFFAEEEDDEFFEFEEDDDDEEFFEFECA?D?EEDEEDFFCEDD'88A?*?CEAE?EECDEAA:?EE?EEFFFFC:?CEEF8:CEA:??EE?:*AEFFEFAEDDEEFECC?AAE\n+@M01368:28:000000000-A5KYY:1:1101:10581:22138/2\n+TACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTAGCTACCCCCAAG\n++\n+??AA?B?ADDDDDDDBFFGGGGHHEHHIHHHHHHIII@HHHHHIIHDEHDFHHHIIHIIHHHHDDCCEEEFFHHHHHHHHGGGGGGGGGGEGG@EGGECEECEECEEGEG3;CCCEGGGGEGEGG?:CEEECE*?EECGGGGGGECECGGCEGECE:CCGECEEEGE?CCGGEGGGGGEGCEECCECECE?C8?CCGEECEGGGGGEGEGEGGGGGGGEEECCCE>GEG\n+@M01368:28:000000000-A5KYY:1:1101:10696:7547/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATA"..b'GTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n++\n+??A?ABBBDDDDDDDEGGGGFGFFHIIIHFGHHDFHHIHIIIIHHIGHHIHHHIIHHHHIHHHGIIIIIIIIIIIIHHHHEHHHHHHHHHHHHFHGHHHHHHHHHHGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGEGGGGEGGGGGGGGGGGGEEEGEGGGGGGE:*.8??CCGGGGGGGGGEGGGEGGGGAGGGGGGGGGGGGGGGGGCC?CG:CECEGGGGCEGGGGGGGGGGGGGG\n+@M01368:28:000000000-A5KYY:1:1106:19331:13430/2\n+GGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATAC\n++\n+??????BBDDBDDDDDGGGGGGIIIIHHHAFHHIIHHHHHIIIIIIIIIIIIIIHFHGHIHIHEEHIHIHHGDEGEGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGG;EEGGGGGGGGGGGEGGGEGGGGGGGGGGGCEGGEGGGGGGGGGGGGGGCGGEGGGGGGGGCEEGDGGGGGG\n+@M01368:28:000000000-A5KYY:1:1106:19484:14339/2\n+GTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCCCTGAAG\n++\n+?????/<BBDDDDBDDEFFFFEFEHFHIIIIH@FHHIGHIHHCDEDGHIHHHFFFDFHHHH=ECEHHIFC@AFHHHHHHHEEFHHHHHHHHHHHEHHFHFFFEEF:BEFFFFEFFEEEEFFE;DEDFFEEF?EFEFEEFEE??AEEEEED?A8A?CA:AE??:0A?0?.*1:A*1:C*AEFFFFCE?8A:?A?CEACFFEA:AE82AEEE*8AEAEFEFFAEECACEEFEFFFFE8AAC?*\n+@M01368:28:000000000-A5KYY:1:1106:19767:21874/2\n+GTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCCCTGAAGTAGGAACCAG\n++\n+?????BBB/BBBBBBBEFFFCEHH9EFEEFGH-7CDGFFHHHHDHHHHHHHHFFDFGHHHHHHHHHHHHHHCEEHHHHEH)5CFCFCCDC?CFHHHHFHFFFEEE>@DDEEEECEEE:A?E>??E?EEEEEEEECEEEEEECEAEA?EA;?EEEAACEEEEEEEEEAAE/::**0:C:CEEEEEEAEAE:A:?AEEEECEEAE?E?8??80.:?EEEEEEEECAC?C?AEC:CE:CE8?**0::AEEEAEC\n+@M01368:28:000000000-A5KYY:1:1106:20079:20293/2\n+ACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATAATGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGA\n++\n+????ABBBDDDDDDDDGGGGGGIFBFFBF>ECDGFFHHHCFGHHIHHHHHIIIIIFHHFHIIHHHHIFHHIIIIIHIFHG-AEHHHHHHIIFHFHHFHHHHHEHHHHFDEGDGGGGGGGGGGGGGGGG@CCGGCACGDGGGCEGGGGGEEGGGCCGGEGEGEECECEC:CED*)0?CCECEEEGECGG:CEG?CEEGCCGGEE?:CGCEEGG\n+@M01368:28:000000000-A5KYY:1:1106:20084:8979/2\n+GTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGC\n++\n+?<???BBBDDDDDEDAFF?FFFHFFCF;C,7CCAEG>@CEEHGHCFFHFFHHGFDFEEA:EFFFHHDFFFHHFFFGHF@CA>CFHFF8E+@DCE7CHHFCCFC@EDFFFEE@BD=BDDAEE@EECEE=BEEE>;A.8>;D?>E?EEEE8:?CE?EA::A?E?EEE>8A)?*:?:8*:**0A80).::CEE?AEC:*:AECEEA8AACEEECC:CAACCAE*4.?8A?EEEEEAEEAE?EC**::A**:CC\n+@M01368:28:000000000-A5KYY:1:1106:20271:14486/2\n+GTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCACTGAAGTAGGAACCAG\n++\n+?????BBBBBBBB?BDEFFFFEHEHAAC>FFHHEHEHGHHHHHHIFFF@FGHHF=FGGGGGFD>EHEGHHIFHEHHIHHBDEFHHHHEHHHHHHHHHFFFFFDEFEEEFFFEEEFEEEEEEEDDEDFFFFECAACEFFEFCEEEAEFFFDFECEEFECEFFFFFEE:AC?CC?*:ACEEFFFFFFFEEE??C?:AEFFACA:ACEDEAEAAAEFEEA?EFCFFEEEEECEECC?*1:?::?EFEA:C?0*?\n+@M01368:28:000000000-A5KYY:1:1106:20363:9345/2\n+CGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCCCTGAAGTAGGA\n++\n+AA?AA?BBDBDDDDDDGGFGFFCFH8CAF,7C@7ADEDHGHHHHHHIHFGGEECCHIGIICFDFHDHHH@EFDFFHHHEFFFEHHHHHHHHEHCGGGGGGGEEGGDGEEEGBGGBGGEGGCCEGGGGGEGGGCCEGGGGC?8?C:C:CCCECCEGCEGGCEGGGGGEG*:CC?CEEEGCEGEEEG?EEE:C?EGD8???CC:?CEGCCGEE?CEGGGGCEEEEE*8??EECGGGG\n'

diff -r 7d34178f2812 -r 9ffcddf6f9c0 test-data/picard_SamToFastq_se.bam

Binary file test-data/picard_SamToFastq_se.bam has changed

diff -r 7d34178f2812 -r 9ffcddf6f9c0 test-data/picard_SamToFastq_se.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_SamToFastq_se.fq Mon Feb 17 10:24:29 2020 -0500

b'@@ -0,0 +1,24944 @@\n+@5967425\n+CGACATATCTTCTTGGTGGTG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@12228434\n+TGAGTAGACTGTCCATCAACT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@28010\n+AGCTTCAAGGTAGTTGGGCGG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@16796783\n+CGTCATATCATCATATTCGGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@1272860\n+AATTCGGCGCCAGTCTGGCAG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@16700436\n+GCTGTGGGCTAGTGTGGATCG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3570674\n+CGAATTCTCTGACTCGTAGCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@11379350\n+TCTTCTTCCTCTTCGGGCACA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@16654356\n+TGCTGTCAAATATTACACTCT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10348751\n+TAAAGATAATATATGTGCTGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@846273\n+GTGTAATTGTTGAACGTTATA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7972861\n+GTGTAATTGTTGAACGTTATA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@2781166\n+AACGGTGTAATTGTTGAACGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@15557255\n+AACGGTGTAATTGTTGAACGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7257564\n+TAACGGTGTAATTGTTGAACG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3194371\n+AATCGTTTTTGCTCACACTGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@2888130\n+CTTACGCCTGACTTTCTTCGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7551686\n+GGCTCCTGGTCGTAGAACGCG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3335624\n+TTGGGCAACGTCCTGTTGGTG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@833212\n+TGGTCACAGCGGTGGTGGCTC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@15554722\n+AATGAACCTGGAGCACTCGCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@15430832\n+CAAATGAACCTGGAGCACTCG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@14876001\n+CCATGGTCTCAGCTCTGAGCT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3993070\n+TTTCTTGCAAGTTGCACGGGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10270334\n+TTGGAGCTTCTACGAAACACT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10106351\n+TACAACTTTGGCAAGAACTGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@6477524\n+ACATGTTTCGCCGTCTTAGTC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7610178\n+CATTTATTTGTGTGCCTGTTG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@5862866\n+ACACTGAGGAGATCTTTGGCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@14864828\n+AGCAGGGCAAAACCTTGGCCG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@889006\n+ACGCGATCCGATCCCCGCACC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@8858638\n+TAGAACGAGCTACAGAAGTCT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@13374520\n+CCAAAGTCTGGGCTACGGCTT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@12993865\n+ACGCAGCAGGACGTGTTCGCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@755815\n+TCCGGGCTGCACTATGGTATC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7709123\n+GGTTTGTGTTTCTGTTCTGAG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7369535\n+TTGTGTCAGTAAGCCAGATGA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@15757583\n+TGTGGGGGCCTGTGTGTGTGG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@1143015\n+TTAAACCCCAACCGAAGGACG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@9570822\n+CGATGAATTGACCTGAACAAG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@15839066\n+AGAAGACTGTTCGCTCTGCGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@1701410\n+AACTGCTCCCCTGTCCGGGAT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3637388\n+AAAAATGATCCAATATTAAAG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@8008088\n+ACACGGGTGAGCAACTGGGGA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3360592\n+GAAGAGCTGAACTGCGCCGCT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@9322340\n+AGTGGGTGACTCATGTGGGGG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3466493\n+TCGTATTATTTTCATTTCACC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@804477\n+TTCTTTCATTTTCGTTTCGTT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@8153037\n+TATTTGGTTTTTATATGACGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@8858893\n+TTTTAGTGAAGAAGGGGTAAA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@13191423\n+TCTTGTTGGTTTCCAGGAACC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10375824\n+AACGCATCGGAACAATTCTGA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@8281341\n+AGATGTTGTTGCTGAAATGGG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@9687787\n+AAATGCACGCTGTAATGGCTT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@11471287\n+GAAATGCCGAGACTGGGATGG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@9010256\n+TCCATCGGAGTTGGCCAGCAT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@5568345\n+GCGGAGCGGATGCATTACAGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@11674899\n+GACGGCAAATTAACTCGACTG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@4845219\n+TAGACAACTGATCAGAATGGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10606244\n+TTTCGCTGGCCAGCACAAGGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3702592\n+CAAAGTTAATATGGAGCGTAT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@12472007\n+TGGAATTTGTATTAGACATCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@8404266\n+CTTCGCATTTGGGCTTCTTTG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@15442808\n+CGTTTTTCTGACACGAGTTCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7856093\n+CAGAAAAACGAACGGCAAAGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@12056649\n+CCGAGATAAGTTGGGGTCTAC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10185605\n+TATGACGGCACGCAGCAACCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@15805'..b'IIIIIIIIIIIIIIIIIIII\n+@16857572\n+TTTTTCAGCTTGGGGAGGTAG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7310142\n+CAGAACTATATGAGCAAAAAC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@12971335\n+CATCAGCATAATGGACGGATT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@9489708\n+TCCGGACTCGCAGATGGAGAC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@6233684\n+ACATCCCAACCACAGGCGGCT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@4288058\n+AGGAGCCGGACACGGAGCAGG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10297754\n+ATCCAAGCCGGACTTACTGCA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@12659489\n+CAGTTAATCCACCGCCAGCTG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@9709709\n+TTCGGGACTAGCCGATCTTCT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@4873191\n+CGGCCAGCCCCACTCCGGATT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@6627160\n+CGAAACTAGTTCGGAGCTACT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@16032842\n+TCGGCACTACCATTGAGGCGG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@1350012\n+CTAAACTGTGCGCCGCGTACC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@12218047\n+TATAACTCTTAAATCAGCTCT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@13555888\n+ATAACGCCTATAACTCTTAAA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7928754\n+ATTACATTACCATCTTAGGCG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3432578\n+ATACACTGAAACAGAAAATGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@11123028\n+AAAGCGAGCTGATCGAACGTC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@11036855\n+TATAGACCCGTTTGACACTTC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@15607689\n+TCGACACACTCAAGACCGTCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3933650\n+GCGGCAAATCTCCAGCCGGAC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3405308\n+CATTTGACACATCCATAGCGG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@8568565\n+TCTTAACACCCGCTCAAGACC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@6430811\n+CAACATCAAGGTCTTAACACC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7445874\n+AAAAGGATTTGATCTCCGTAC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@11162747\n+AGCGGGTAATGAATTGGGAGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@11860246\n+CTAAACATACAGGCCAAGAGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10509986\n+GAGTAACCAAGACTTTGATCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10666343\n+TTAAGTGTCGACCAAGAGGCA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@4958049\n+CCACAACGCGATCTTCTCGCT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@31059\n+TCGGGCCAAGAACCAGGGAAG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@5862871\n+CAATCGGGCCAAGAACCAGGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@6186109\n+CAATCGGGCCAAGAACCAGGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@5060884\n+AATTTGAAGAGCAATCGGGCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3578932\n+TGTTTTGCCTGTCGCGCAGCT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@16700868\n+TGTAGTTAGCCAGGTTGTTTT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7522487\n+GAACTAGCCGCGGAATCGCTG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@14594233\n+TCGACGAGGAACTATCCGAGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@12304006\n+TCCTTGCCGAAGACGGACCCG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@6537865\n+GATCAAAATCAGGGGGCTGCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@7552086\n+CAGCACGATTTCGTATTCGAC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@4280565\n+AGCTGAATTCTACGTAGTCGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@16694848\n+CTTTGAGCTTTGACTGACTGA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@2121028\n+AAAATATTCCTCCCTGGCATG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@6279989\n+ATCTAAATGTTGCCTATTGTA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@16121197\n+TTTCATAGAGATCCTTAGGTT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@1180275\n+TTTTCTATGTGCCGCGCGTGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@15393395\n+AAAACTTCGGAAATTCAGCTG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@15355149\n+TTCGATCTGTTCCTGTCCGTC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10040236\n+CTTCTCTTTATATCCGTTACT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@6300654\n+TTTAATGTTGGTGCTGAGAGG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@6429688\n+CGGGTACGTCCAAAGTTTATG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@16755914\n+ACAGCTCCCCGTTTTGCGACC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@2658933\n+TGTCCGTGGAAGGTCTGGCCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@719673\n+TGATTACGTGACGGAGAAACC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@11230856\n+TTTTGAGTACTCGCTGTGCGA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@14546216\n+TTAAAGTCGCTCGCTAAGCCC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3424368\n+CGGAACACTCAAGTGAGGACC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10691675\n+CAAGATCACTTAAGGGGCCAG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@1646671\n+TTGGCCTGTGGGCCGCGCGGC\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@8517389\n+TCGGTACGGTTGGCCTGTGGG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@6392681\n+TATCTGGTCGAGTTGGGCACA\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@1586697\n+AAATCGGTATTTATCAAGCGT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@13867766\n+AGTGTGAGCTATGTATGTTTG\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@5258744\n+CCAATCTATAATATTCGGGCT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@3227807\n+GTAATAAACAATCTTGTACTT\n++\n+IIIIIIIIIIIIIIIIIIIII\n+@10835612\n+GCGCAGTTGAATATTTGGGAC\n++\n+IIIIIIIIIIIIIIIIIIIII\n'