| Next changeset 1:0a5c7992b1ac (2017-03-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f |
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added:
abyss-pe.xml test-data/abyss-contigs1.fa test-data/abyss-scaffolds1.fa test-data/abyss-stats1.tab test-data/abyss-stats2.tab test-data/abyss-unitigs1.fa test-data/abyss-unitigs2.fa test-data/assembly_sample-R1.fastq test-data/assembly_sample-R2.fastq test-data/coverage1.hist test-data/coverage2.hist test-data/empty_file.fasta tool_dependencies.xml |
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| diff -r 000000000000 -r f048033da666 abyss-pe.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abyss-pe.xml Fri Jun 19 09:26:16 2015 -0400 |
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| b'@@ -0,0 +1,244 @@\n+<tool id="abyss-pe" name="ABySS" version="1.9.0.0">\n+ <description>de novo sequence assembler</description>\n+ <macros>\n+ <xml name="reads_conditional">\n+ <conditional name="reads">\n+ <param name="reads_selector" type="select" label="Type of paired-end datasets">\n+ <option value="paired">2 separate datasets</option>\n+ <option value="paired_collection">1 paired dataset collection</option>\n+ <option value="paired_il">1 dataset of interleaved reads</option>\n+ </param>\n+ <when value="paired">\n+ <param name="reads1" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads 1" />\n+ <param name="reads2" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads 2" />\n+ </when>\n+ <when value="paired_collection">\n+ <param name="reads_coll" type="data_collection" collection_type="paired" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads collection" />\n+ </when>\n+ <when value="paired_il">\n+ <param name="reads_il" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Interleaved paired-end reads" />\n+ </when>\n+ </conditional>\n+ </xml>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="1.9.0">abyss</requirement>\n+ </requirements>\n+ <stdio>\n+ <!-- Anything other than zero is an error -->\n+ <exit_code range="1:" />\n+ <!-- In case the return code has not been set propery check stderr too -->\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ </stdio>\n+ <version_command>ABYSS --version | head -n 1</version_command>\n+ <command>\n+abyss-pe name=abyss j=\\${GALAXY_SLOTS:-1} k=$k\n+#if str($K)\n+ K=$K\n+#end if\n+#if str($q)\n+ q=$q\n+#end if\n+#if str($Q)\n+ Q=$Q\n+#end if\n+#if str($e)\n+ e=$e\n+#end if\n+#if str($E)\n+ E=$E\n+#end if\n+#if str($t)\n+ t=$t\n+#end if\n+#if str($c)\n+ c=$c\n+#end if\n+#if str($b)\n+ b=$b\n+#end if\n+#if $SS\n+ SS=--SS\n+#end if\n+#if str($m)\n+ m=$m\n+#end if\n+#if str($p)\n+ p=$p\n+#end if\n+#if str($a)\n+ a=$a\n+#end if\n+#if str($l)\n+ l=$l\n+#end if\n+#if str($s)\n+ s=$s\n+#end if\n+#if str($n)\n+ n=$n\n+#end if\n+#if str($d)\n+ d=$d\n+#end if\n+#if str($S)\n+ S=$S\n+#end if\n+#if str($N)\n+ N=$N\n+#end if\n+#if $lib_repeat\n+ lib=\'\n+ #for $i in range(len($lib_repeat))\n+ lib$i\n+ #end for\n+ \'\n+ #for $i, $v in enumerate($lib_repeat)\n+ #if $v.reads.reads_selector == \'paired\'\n+ lib${i}=\'${v.reads.reads1} ${v.reads.reads2}\'\n+ #elif $v.reads.reads_selector == \'paired_collection\'\n+ lib${i}=\'${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}\'\n+ #else\n+ lib${i}=\'${v.reads.reads_il}\'\n+ #end if\n+ #end for\n+#end if\n+#if str($se_reads) != \'None\'\n+ se=\'\n+ #for $v in $se_reads\n+ $v\n+ #end for\n+ \'\n+#end if\n+#if $mp_repeat\n+ mp=\'\n+ #for $i in range(len($mp_repeat))\n+ mp$i\n+ #end for\n+ \'\n+ #for $i, $v in enumerate($mp_repeat)\n+ #if $v.reads.reads_selector == \'paired\'\n+ mp${i}=\'${v.reads.reads1} ${v.reads.reads2}\'\n+ #elif $v.reads.reads_selector == \'paired_collection\'\n+ mp${i}=\'${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}\'\n+ #else\n+ mp${i}=\'${v.reads.reads_il}\'\n+ #end if\n+ #end for\n+#end if\n+#if str($long_seqs) != \'None\'\n+ long=\'\n+ #for $v in $long_seqs\n+ $v\n+ #end for\n+ \'\n+#end if\n+ </command>\n+\n+ <inputs>\n+ <repeat name="lib_repeat" title="Paired-end library" help="(lib)">\n+ <expand macro="reads_conditional" />\n+ </repeat>\n+ <param name="se_reads" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Single-end reads" help="(se)" />\n+ <repeat name="mp_repeat" title="Mate-pair library" help="The '..b'lp="Defaults to the value of n (N)" />\n+ </inputs>\n+\n+ <outputs>\n+ <data name="unitigs" format="fasta" label="${tool.name} on ${on_string}: unitigs" from_work_dir="abyss-unitigs.fa" />\n+ <data name="contigs_outfile" format="fasta" label="${tool.name} on ${on_string}: contigs" from_work_dir="abyss-contigs.fa">\n+ <filter>lib_repeat</filter>\n+ </data>\n+ <data name="scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-scaffolds.fa">\n+ <filter>lib_repeat or mp_repeat</filter>\n+ </data>\n+ <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" />\n+ <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />\n+ <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" />\n+ <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <repeat name="lib_repeat">\n+ <conditional name="reads">\n+ <param name="reads_selector" value="paired" />\n+ <param name="reads1" ftype="fastqsanger" value="assembly_sample-R1.fastq" />\n+ <param name="reads2" ftype="fastqsanger" value="assembly_sample-R2.fastq" />\n+ </conditional>\n+ </repeat>\n+ <param name="k" value="50" />\n+ <output name="unitigs" file="abyss-unitigs1.fa" />\n+ <output name="contigs_outfile" file="abyss-contigs1.fa" />\n+ <output name="scaffolds" file="abyss-scaffolds1.fa" />\n+ <output name="bubbles" file="empty_file.fasta" />\n+ <output name="indels" file="empty_file.fasta" />\n+ <output name="coverage_histogram_outfile" file="coverage1.hist" />\n+ <output name="stats" file="abyss-stats1.tab" />\n+ </test>\n+ <test>\n+ <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" />\n+ <param name="k" value="50" />\n+ <output name="unitigs" file="abyss-unitigs2.fa" />\n+ <output name="bubbles" file="empty_file.fasta" />\n+ <output name="indels" file="empty_file.fasta" />\n+ <output name="coverage_histogram_outfile" file="coverage2.hist" />\n+ <output name="stats" file="abyss-stats2.tab" />\n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+`ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes.\n+\n+**Input**\n+\n+Input files should be FASTA or FASTQ files.\n+\n+For paired reads, a pair of reads must be named with the suffixes /1 and /2 to identify the first and second read, or the reads may be named identically. The paired reads may be in separate files or interleaved in a single file.\n+\n+At least a paired-end library or a single-end library must be provided.\n+\n+Contigs are generated only if at least a paired-end library is provided. Scaffolds are generated only if at least a paired-end library or a mate-pair library is provided.\n+\n+**Description**\n+\n+This tool performs the complete ABySS pipeline using abyss-pe, described in https://github.com/bcgsc/abyss/blob/master/doc/flowchart.pdf .\n+\n+**License and citation**\n+\n+This Galaxy tool is Copyright \xc2\xa9 2015 `The Genome Analysis Centre (TGAC)`_ and is released under the `MIT license`_.\n+\n+.. _The Genome Analysis Centre (TGAC): http://www.tgac.ac.uk/\n+.. _MIT license: http://opensource.org/licenses/MIT\n+\n+You can use this tool only if you agree to the license terms of: `ABySS`_.\n+\n+.. _ABySS: http://www.bcgsc.ca/platform/bioinfo/software/abyss\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1101/gr.089532.108</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r f048033da666 test-data/abyss-contigs1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abyss-contigs1.fa Fri Jun 19 09:26:16 2015 -0400 |
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| @@ -0,0 +1,2 @@ +>0 556 6128 +GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC |
| b |
| diff -r 000000000000 -r f048033da666 test-data/abyss-scaffolds1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abyss-scaffolds1.fa Fri Jun 19 09:26:16 2015 -0400 |
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| @@ -0,0 +1,2 @@ +>0 556 6128 +GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC |
| b |
| diff -r 000000000000 -r f048033da666 test-data/abyss-stats1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abyss-stats1.tab Fri Jun 19 09:26:16 2015 -0400 |
| b |
| @@ -0,0 +1,4 @@ +n n:500 L50 min N80 N50 N20 E-size max sum name +1 1 1 556 556 556 556 556 556 556 abyss-unitigs.fa +1 1 1 556 556 556 556 556 556 556 abyss-contigs.fa +1 1 1 556 556 556 556 556 556 556 abyss-scaffolds.fa |
| b |
| diff -r 000000000000 -r f048033da666 test-data/abyss-stats2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abyss-stats2.tab Fri Jun 19 09:26:16 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +n n:500 L50 min N80 N50 N20 E-size max sum name +1 1 1 556 556 556 556 556 556 556 abyss-unitigs.fa |
| b |
| diff -r 000000000000 -r f048033da666 test-data/abyss-unitigs1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abyss-unitigs1.fa Fri Jun 19 09:26:16 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>0 556 6128 +GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC |
| b |
| diff -r 000000000000 -r f048033da666 test-data/abyss-unitigs2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abyss-unitigs2.fa Fri Jun 19 09:26:16 2015 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>0 556 6128 +GAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC |
| b |
| diff -r 000000000000 -r f048033da666 test-data/assembly_sample-R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly_sample-R1.fastq Fri Jun 19 09:26:16 2015 -0400 |
| b |
| b'@@ -0,0 +1,604 @@\n+@HWI-ST745_0097:7:1101:1001:1000#0/1\n+GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTT\n++HWI-ST745_0097:7:1101:1001:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1002:1000#0/1\n+AAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTA\n++HWI-ST745_0097:7:1101:1002:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1003:1000#0/1\n+AAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAG\n++HWI-ST745_0097:7:1101:1003:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1004:1000#0/1\n+AAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGT\n++HWI-ST745_0097:7:1101:1004:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1005:1000#0/1\n+AACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTG\n++HWI-ST745_0097:7:1101:1005:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1006:1000#0/1\n+ACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGG\n++HWI-ST745_0097:7:1101:1006:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1007:1000#0/1\n+CGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGT\n++HWI-ST745_0097:7:1101:1007:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1008:1000#0/1\n+GCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTG\n++HWI-ST745_0097:7:1101:1008:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1009:1000#0/1\n+CGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGA\n++HWI-ST745_0097:7:1101:1009:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1010:1000#0/1\n+GCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAG\n++HWI-ST745_0097:7:1101:1010:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1011:1000#0/1\n+CTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGT\n++HWI-ST745_0097:7:1101:1011:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1012:1000#0/1\n+TTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTC\n++HWI-ST745_0097:7:1101:1012:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1013:1000#0/1\n+TGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCG\n++HWI-ST745_0097:7:1101:1013:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1014:1000#0/1\n+GCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGT\n++HWI-ST745_0097:7:1101:1014:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1015:1000#0/1\n+CAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTC\n++HWI-ST745_0097:7:1101:1015:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1016:1000#0/1\n+AGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCG\n++HWI-ST745_0097:7:1101:1016:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1017:1000#0/1\n+GATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGG\n++HWI-ST745_0097:7:1101:1017:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1018:1000#0/1'..b'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1135:1000#0/1\n+GACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCA\n++HWI-ST745_0097:7:1101:1135:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1136:1000#0/1\n+CCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATC\n++HWI-ST745_0097:7:1101:1136:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1137:1000#0/1\n+GTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCG\n++HWI-ST745_0097:7:1101:1137:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1138:1000#0/1\n+TTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCA\n++HWI-ST745_0097:7:1101:1138:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1139:1000#0/1\n+GGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACT\n++HWI-ST745_0097:7:1101:1139:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1140:1000#0/1\n+TTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCC\n++HWI-ST745_0097:7:1101:1140:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1142:1000#0/1\n+CCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGA\n++HWI-ST745_0097:7:1101:1142:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1141:1000#0/1\n+CGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAA\n++HWI-ST745_0097:7:1101:1141:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1145:1000#0/1\n+AACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGT\n++HWI-ST745_0097:7:1101:1145:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1143:1000#0/1\n+ACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTT\n++HWI-ST745_0097:7:1101:1143:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1144:1000#0/1\n+CTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTG\n++HWI-ST745_0097:7:1101:1144:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1146:1000#0/1\n+CTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTG\n++HWI-ST745_0097:7:1101:1146:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1147:1000#0/1\n+TGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGC\n++HWI-ST745_0097:7:1101:1147:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1148:1000#0/1\n+CCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACC\n++HWI-ST745_0097:7:1101:1148:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1149:1000#0/1\n+CATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCA\n++HWI-ST745_0097:7:1101:1149:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1150:1000#0/1\n+ATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAG\n++HWI-ST745_0097:7:1101:1150:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1151:1000#0/1\n+TGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGC\n++HWI-ST745_0097:7:1101:1151:1000#0/1\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r f048033da666 test-data/assembly_sample-R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly_sample-R2.fastq Fri Jun 19 09:26:16 2015 -0400 |
| b |
| b'@@ -0,0 +1,604 @@\n+@HWI-ST745_0097:7:1101:1001:1000#0/2\n+GCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTC\n++HWI-ST745_0097:7:1101:1001:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1002:1000#0/2\n+TTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAA\n++HWI-ST745_0097:7:1101:1002:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1003:1000#0/2\n+ATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAG\n++HWI-ST745_0097:7:1101:1003:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1004:1000#0/2\n+CAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGC\n++HWI-ST745_0097:7:1101:1004:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1005:1000#0/2\n+CCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCC\n++HWI-ST745_0097:7:1101:1005:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1006:1000#0/2\n+CCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTC\n++HWI-ST745_0097:7:1101:1006:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1007:1000#0/2\n+AAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGC\n++HWI-ST745_0097:7:1101:1007:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1008:1000#0/2\n+TGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGT\n++HWI-ST745_0097:7:1101:1008:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1009:1000#0/2\n+GCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTC\n++HWI-ST745_0097:7:1101:1009:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1010:1000#0/2\n+GGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGG\n++HWI-ST745_0097:7:1101:1010:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1011:1000#0/2\n+TTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGG\n++HWI-ST745_0097:7:1101:1011:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1012:1000#0/2\n+CTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATA\n++HWI-ST745_0097:7:1101:1012:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1013:1000#0/2\n+CAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGC\n++HWI-ST745_0097:7:1101:1013:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1014:1000#0/2\n+CCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGA\n++HWI-ST745_0097:7:1101:1014:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1015:1000#0/2\n+CTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTA\n++HWI-ST745_0097:7:1101:1015:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1016:1000#0/2\n+GTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCG\n++HWI-ST745_0097:7:1101:1016:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1017:1000#0/2\n+CATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGA\n++HWI-ST745_0097:7:1101:1017:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1018:1000#0/2'..b'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1135:1000#0/2\n+ACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCAT\n++HWI-ST745_0097:7:1101:1135:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1136:1000#0/2\n+TTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTAC\n++HWI-ST745_0097:7:1101:1136:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1137:1000#0/2\n+GTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGA\n++HWI-ST745_0097:7:1101:1137:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1138:1000#0/2\n+CTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCT\n++HWI-ST745_0097:7:1101:1138:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1139:1000#0/2\n+GCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCT\n++HWI-ST745_0097:7:1101:1139:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1140:1000#0/2\n+CGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGG\n++HWI-ST745_0097:7:1101:1140:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1142:1000#0/2\n+GAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTC\n++HWI-ST745_0097:7:1101:1142:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1141:1000#0/2\n+TGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTG\n++HWI-ST745_0097:7:1101:1141:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1145:1000#0/2\n+GATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAG\n++HWI-ST745_0097:7:1101:1145:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1143:1000#0/2\n+AGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGC\n++HWI-ST745_0097:7:1101:1143:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1144:1000#0/2\n+TGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCG\n++HWI-ST745_0097:7:1101:1144:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1146:1000#0/2\n+TGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAA\n++HWI-ST745_0097:7:1101:1146:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1147:1000#0/2\n+CTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCC\n++HWI-ST745_0097:7:1101:1147:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1148:1000#0/2\n+GATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAG\n++HWI-ST745_0097:7:1101:1148:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1149:1000#0/2\n+CTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATG\n++HWI-ST745_0097:7:1101:1149:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1150:1000#0/2\n+TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACC\n++HWI-ST745_0097:7:1101:1150:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-ST745_0097:7:1101:1151:1000#0/2\n+AACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCG\n++HWI-ST745_0097:7:1101:1151:1000#0/2\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r f048033da666 test-data/coverage1.hist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage1.hist Fri Jun 19 09:26:16 2015 -0400 |
| b |
| @@ -0,0 +1,27 @@ +1 4 +2 8 +3 6 +4 13 +5 20 +6 36 +7 70 +8 56 +9 60 +10 66 +11 56 +12 32 +13 27 +14 44 +15 24 +16 25 +17 39 +18 28 +19 23 +20 11 +21 12 +22 5 +23 5 +24 2 +25 2 +26 2 +27 16 |
| b |
| diff -r 000000000000 -r f048033da666 test-data/coverage2.hist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage2.hist Fri Jun 19 09:26:16 2015 -0400 |
| b |
| @@ -0,0 +1,27 @@ +1 4 +2 8 +3 6 +4 13 +5 20 +6 36 +7 70 +8 56 +9 60 +10 66 +11 56 +12 32 +13 27 +14 44 +15 24 +16 25 +17 39 +18 28 +19 23 +20 11 +21 12 +22 5 +23 5 +24 2 +25 2 +26 2 +27 16 |
| b |
| diff -r 000000000000 -r f048033da666 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 19 09:26:16 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="abyss" version="1.9.0"> + <repository changeset_revision="ded58f1da91c" name="package_abyss_1_9_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |