Mercurial > repos > devteam > fastq_combiner

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_combiner.py	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,49 @@
+#Dan Blankenberg
+import sys, os, shutil
+from galaxy_utils.sequence.fastq import fastqWriter, fastqSequencingRead, fastqCombiner, fastqFakeFastaScoreReader
+from galaxy_utils.sequence.fasta import fastaReader, fastaNamedReader
+
+def main():
+    #Read command line arguments
+    fasta_filename = sys.argv[1]
+    fasta_type = sys.argv[2] or 'fasta' #should always be fasta or csfasta? what if txt?
+    qual_filename = sys.argv[3]
+    qual_type = sys.argv[4] or 'qualsanger' #qual454 qualsolid
+    output_filename = sys.argv[5]
+    force_quality_encoding = sys.argv[6]
+    if force_quality_encoding == 'None':
+        force_quality_encoding = None
+
+    format = 'sanger'
+    if fasta_type == 'csfasta' or qual_type == 'qualsolid':
+        format = 'cssanger'
+    elif qual_type == 'qualsolexa':
+        format = 'solexa'
+    elif qual_type == 'qualillumina':
+        format = 'illumina'
+
+    out = fastqWriter( open( output_filename, 'wb' ), format = format, force_quality_encoding = force_quality_encoding )
+    if qual_filename == 'None':
+        qual_input = fastqFakeFastaScoreReader( format, quality_encoding = force_quality_encoding )
+    else:
+        qual_input = fastaNamedReader( open( qual_filename, 'rb' )  )
+
+    fastq_combiner = fastqCombiner( format )
+    i = None
+    skip_count = 0
+    for i, sequence in enumerate( fastaReader( open( fasta_filename, 'rb' ) ) ):
+        quality = qual_input.get( sequence )
+        if quality:
+            fastq_read = fastq_combiner.combine( sequence, quality )
+            out.write( fastq_read )
+        else:
+            skip_count += 1
+    out.close()
+    if i is None:
+        print "Your file contains no valid FASTA sequences."
+    else:
+        print qual_input.has_data()
+        print 'Combined %s of %s sequences with quality scores (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 )
+
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_combiner.xml	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,80 @@
+<tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.0.1">
+  <description>into FASTQ</description>
+  <requirements>
+    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
+  </requirements>
+  <command interpreter="python">fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding'</command>
+  <inputs>
+    <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" />
+    <param name="qual_file" type="data" format="qual" label="Quality Score File" optional="True" />
+    <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
+      <option value="None">Use Source Encoding</option>
+      <option value="ascii" selected="True">ASCII</option>
+      <option value="decimal">Decimal</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="output_file" format="fastqsanger">
+      <change_format>
+        <when input_dataset="fasta_file" attribute="extension" value="csfasta" format="fastqcssanger" />
+        <when input_dataset="qual_file" attribute="extension" value="qualsolid" format="fastqcssanger" />
+        <when input_dataset="qual_file" attribute="extension" value="qualsolexa" format="fastqsolexa" />
+        <when input_dataset="qual_file" attribute="extension" value="qualillumina" format="fastqillumina" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
+      <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
+      <param name="force_quality_encoding" value="None" />
+      <output name="output_file" file="combine_phiX_out_1.fastqcssanger" />
+    </test>
+    <test>
+      <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
+      <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
+      <param name="force_quality_encoding" value="ascii" />
+      <output name="output_file" file="combine_phiX_out_2.fastqcssanger" />
+    </test>
+    <test>
+      <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
+      <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
+      <param name="force_quality_encoding" value="None" />
+      <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
+    </test>
+    <test>
+      <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
+      <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
+      <param name="force_quality_encoding" value="decimal" />
+      <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" />
+    </test>
+    <test>
+      <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
+      <param name="qual_file" />
+      <param name="force_quality_encoding" value="decimal" />
+      <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" />
+    </test>
+    <test>
+      <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
+      <param name="qual_file" />
+      <param name="force_quality_encoding" value="ascii" />
+      <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqcssanger" />
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read.
+
+Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqcssanger (when a csfasta is provided) with each quality score being the maximal allowed value (93).
+
+Use this tool, for example, to convert 454-type output to FASTQ.
+
+------
+
+**Citation**
+
+If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/combine_phiX_out_1.fastqcssanger	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,576 @@
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++
+17 30 31 31 30 32 31 30 23 27 21 27 25 24 23 20 28 24 24 24 24 24 28 28 33 18 27 20 27 27 11 22 30 29 24
+@1831_575_1535_F3
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++
+31 33 28 31 27 31 31 33 30 25 32 31 31 28 29 31 30 21 23 31 28 30 31 20 30 22 26 25 21 27 27 26 29 20 27
+@1831_575_1724_F3
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++
+24 27 33 13 10 31 8 11 17 9 13 4 8 8 8 19 4 17 31 26 22 2 4 7 4 10 3 23 8 8 23 20 4 5 20
+@1831_575_1829_F3
+T21033321320111321230233302313101021
++
+17 17 7 9 6 4 13 18 3 10 22 8 31 5 4 3 6 18 9 10 9 2 14 2 14 9 10 15 13 28 5 2 8 10 15
+@1831_575_1898_F3
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++
+31 33 29 31 31 5 16 14 8 8 6 19 15 8 4 2 23 14 13 4 2 23 3 7 7 2 26 19 6 3 6 21 18 11 11
+@1831_575_1964_F3
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++
+16 29 18 24 8 31 17 27 17 14 31 10 24 30 17 28 5 8 29 29 31 9 21 17 28 20 5 17 27 19 17 13 6 30 10
+@1831_576_32_F3
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++
+10 27 29 30 29 30 28 22 27 17 8 20 17 17 26 29 27 27 31 19 15 31 29 22 15 19 27 29 20 28 17 18 31 10 5
+@1831_576_74_F3
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++
+23 28 31 31 30 31 29 7 30 30 27 33 20 30 31 31 31 24 27 31 29 27 10 29 27 26 31 6 26 29 21 24 21 16 30
+@1831_576_86_F3
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++
+22 23 16 16 8 17 25 9 13 10 10 20 27 14 25 18 10 19 18 24 17 19 9 8 8 14 25 11 21 5 17 24 8 17 14
+@1831_576_89_F3
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++
+17 8 21 24 10 11 6 13 19 28 12 11 29 14 29 7 9 3 2 8 18 15 18 15 9 6 7 11 4 8 17 2 2 3 11
+@1831_576_266_F3
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++
+27 31 31 30 28 26 27 30 22 28 31 29 24 11 29 31 16 3 5 5 23 24 3 14 25 29 22 6 18 16 22 23 4 5 21
+@1831_576_327_F3
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++
+27 31 30 31 21 31 31 26 27 31 30 29 27 31 29 28 28 18 31 25 28 28 27 18 31 31 29 20 18 27 24 29 27 21 28
+@1831_576_331_F3
+T32012133301311223023011232112333030
++
+26 12 17 8 10 7 9 13 9 16 14 26 20 4 13 12 24 5 2 14 16 6 10 7 3 9 3 2 2 7 8 4 14 3 13
+@1831_576_387_F3
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++
+14 23 8 13 3 20 2 16 2 9 4 13 3 2 2 13 9 2 3 4 2 2 12 4 11 10 11 16 2 5 4 13 4 8 8
+@1831_576_406_F3
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++
+27 19 27 29 4 4 16 19 25 9 19 21 20 21 8 5 27 17 20 16 5 17 10 18 2 5 16 24 11 21 5 19 29 20 7
+@1831_576_449_F3
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++
+7 10 6 5 6 13 11 11 3 14 10 13 8 3 3 23 5 4 2 10 30 5 11 2 8 12 5 2 2 2 22 11 10 2 9
+@1831_576_519_F3
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++
+28 28 19 21 27 24 22 31 29 17 14 21 30 26 17 27 19 32 23 23 16 29 24 16 17 16 10 27 16 14 19 13 24 10 22
+@1831_576_603_F3
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++
+31 31 19 21 28 31 34 13 30 30 27 32 22 24 31 31 26 12 27 31 31 29 17 24 33 30 29 20 20 27 33 22 20 24 23
+@1831_576_655_F3
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++
+28 31 32 32 24 31 31 27 21 9 29 31 31 20 14 27 31 29 24 6 28 26 29 22 10 31 30 24 29 14 24 26 10 11 4
+@1831_576_677_F3
+T13330131023320301031013230210103022
++
+21 17 24 15 5 14 9 15 2 5 6 5 11 13 17 6 2 5 9 3 5 7 6 2 12 4 7 3 9 2 4 3 8 2 4
+@1831_576_718_F3
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++
+3 19 2 2 2 3 15 2 2 2 4 7 2 2 2 2 2 2 2 2 2 11 2 2 2 2 4 2 2 2 2 3 2 2 2
+@1831_576_722_F3
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++
+7 9 11 12 11 2 2 13 8 9 5 7 9 16 4 9 7 4 7 12 17 2 10 8 12 2 13 5 12 2 4 4 3 6 8
+@1831_576_754_F3
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++
+13 19 14 14 2 7 13 3 8 6 6 11 29 7 5 2 16 3 27 11 2 2 4 7 7 11 2 20 30 2 15 9 4 16 9
+@1831_576_815_F3
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++
+27 18 29 31 30 24 29 31 30 33 28 29 28 26 29 32 30 30 30 28 29 25 17 20 28 19 13 17 20 30 21 27 20 22 13
+@1831_576_882_F3
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++
+30 17 21 30 23 30 31 25 19 29 31 29 24 21 30 30 27 27 28 20 6 16 27 29 24 23 19 21 28 27 24 27 16 29 23
+@1831_576_898_F3
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++
+28 31 31 34 17 30 34 29 30 27 29 31 23 23 21 33 30 26 30 13 30 30 23 22 28 33 27 23 27 16 20 30 30 28 13
+@1831_576_923_F3
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++
+22 21 13 20 16 28 26 13 21 24 24 27 24 21 29 26 26 19 24 27 26 26 16 16 26 27 31 20 24 25 24 28 21 19 22
+@1831_576_930_F3
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++
+17 2 9 15 13 17 5 13 25 7 7 2 6 16 19 6 2 2 12 8 2 4 3 3 17 4 2 3 14 16 5 2 4 14 2
+@1831_576_1019_F3
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++
+17 27 3 29 3 11 16 11 5 10 10 5 31 11 13 8 6 10 14 10 2 24 6 21 24 14 21 6 17 7 10 12 6 24 12
+@1831_576_1068_F3
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++
+25 29 29 27 28 19 30 26 31 22 28 30 30 24 30 26 24 29 20 31 24 30 25 23 31 25 28 20 6 26 22 26 6 2 19
+@1831_576_1131_F3
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++
+16 15 19 31 2 31 14 31 11 19 29 24 30 17 10 30 16 20 22 16 31 6 11 29 28 26 7 22 20 24 26 9 24 17 27
+@1831_576_1168_F3
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++
+29 31 34 34 21 31 31 17 30 24 28 29 22 30 26 22 21 27 26 19 21 22 31 26 24 11 15 4 17 21 6 6 11 19 3
+@1831_576_1207_F3
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++
+4 3 29 17 11 7 5 30 19 30 7 11 31 25 27 5 11 31 29 30 3 5 25 23 32 4 4 28 15 13 4 11 20 24 22
+@1831_576_1289_F3
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++
+31 24 27 29 16 33 31 31 26 22 31 31 21 21 18 28 28 17 23 11 20 6 25 23 27 27 11 13 28 17 29 29 13 20 15
+@1831_576_1329_F3
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++
+27 29 5 15 11 23 22 15 14 32 31 31 14 20 13 26 28 26 25 6 5 31 18 6 5 3 3 4 11 10 2 7 3 5 17
+@1831_576_1367_F3
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++
+30 30 31 31 27 29 31 31 28 31 27 31 27 28 31 29 31 30 30 24 25 30 27 28 29 28 27 23 26 20 24 31 22 23 22
+@1831_576_1416_F3
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++
+10 6 26 30 13 13 16 13 27 31 6 13 28 10 21 13 20 30 22 27 15 12 30 22 26 7 4 28 29 20 21 13 24 23 31
+@1831_576_1461_F3
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++
+2 16 5 22 19 2 7 2 7 5 2 2 3 2 11 6 2 2 2 4 2 4 4 2 9 2 5 4 4 2 2 4 4 4 6
+@1831_576_1605_F3
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++
+21 27 31 34 31 31 29 16 26 31 25 26 27 27 31 31 24 31 30 30 30 24 27 18 30 20 12 17 16 28 19 23 22 22 11
+@1831_576_1664_F3
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++
+31 31 30 29 30 31 28 32 25 31 31 29 31 28 6 28 27 29 28 8 13 29 28 24 9 23 8 7 22 2 14 10 10 26 8
+@1831_576_1671_F3
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++
+31 31 30 31 20 29 31 31 23 5 23 30 17 20 2 5 8 5 20 5 5 8 16 20 5 5 11 5 19 4 5 11 5 21 4
+@1831_576_1729_F3
+T11233312313010012320101302101023030
++
+31 30 31 30 27 30 27 31 29 32 30 14 28 28 30 29 30 22 29 30 31 23 27 30 31 29 24 24 26 29 27 10 15 28 29
+@1831_576_1880_F3
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++
+15 20 16 20 14 22 24 17 11 25 11 22 14 4 14 15 20 11 4 3 8 25 10 2 23 4 17 7 16 22 20 19 8 8 18
+@1831_576_1982_F3
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++
+11 31 31 30 31 11 32 29 27 31 24 31 28 30 31 24 33 28 23 27 21 31 31 21 31 17 27 32 30 29 13 22 27 10 31
+@1831_576_1987_F3
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++
+8 2 2 7 8 7 2 5 2 2 8 4 8 14 12 2 4 3 16 16 2 4 18 29 6 2 2 5 3 11 2 3 3 6 10
+@1831_576_2014_F3
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++
+31 31 31 24 11 33 17 24 12 20 29 6 30 11 10 30 22 24 10 14 32 6 26 6 17 31 6 20 5 14 24 11 21 5 16
+@1831_576_2028_F3
+T20131211210311112023201213120201100
++
+20 27 29 24 29 20 6 17 7 5 22 15 22 13 23 2 5 5 18 24 11 15 4 22 14 2 7 2 11 9 4 5 20 9 10
+@1831_577_40_F3
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++
+24 17 14 19 7 6 13 6 8 7 27 9 30 2 3 8 4 5 27 11 14 18 24 27 7 13 17 11 10 27 28 31 21 16 16
+@1831_577_119_F3
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++
+24 29 30 34 16 16 8 12 16 14 8 2 26 2 14 11 23 20 15 9 10 13 10 3 3 20 20 20 15 10 4 12 13 19 15
+@1831_577_133_F3
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++
+14 19 31 29 29 30 28 16 30 25 10 29 31 15 22 31 31 29 27 29 31 9 27 10 16 31 16 20 8 24 21 6 17 3 8
+@1831_577_255_F3
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++
+22 27 28 23 22 31 29 21 24 4 9 9 2 5 2 12 10 3 13 2 5 5 2 10 3 12 10 4 5 4 13 11 4 20 2
+@1831_577_281_F3
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++
+22 12 25 33 26 23 31 28 26 29 22 31 29 19 30 28 30 10 21 20 24 30 26 20 27 22 30 26 24 31 23 7 29 25 30
+@1831_577_288_F3
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++
+20 26 14 22 24 30 30 5 28 33 25 25 17 24 23 9 21 13 22 14 10 19 5 17 16 11 22 11 21 30 13 22 2 6 21
+@1831_577_322_F3
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++
+24 28 26 29 19 20 15 21 26 17 20 20 19 21 19 12 27 2 22 10 16 24 19 5 17 27 30 21 20 24 21 23 8 22 14
+@1831_577_362_F3
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++
+21 17 33 30 25 31 30 31 27 30 24 20 23 28 11 18 25 11 24 15 25 5 6 12 24 24 11 21 27 20 13 7 3 10 21
+@1831_577_382_F3
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++
+16 17 24 20 22 14 25 16 8 8 28 22 21 7 9 17 19 26 11 18 10 25 27 13 5 13 5 12 28 16 28 17 14 20 9
+@1831_577_464_F3
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++
+18 28 27 22 14 27 23 17 21 8 29 2 13 6 5 19 17 15 19 10 20 2 14 15 19 16 13 22 9 24 16 5 22 20 21
+@1831_577_488_F3
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++
+25 19 23 13 11 9 29 21 20 21 21 27 30 23 28 27 28 27 17 29 21 26 24 19 29 26 28 24 29 31 23 24 17 19 31
+@1831_577_511_F3
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++
+2 22 14 10 5 3 25 27 22 4 21 11 3 3 4 6 4 14 10 8 2 3 22 7 7 5 9 18 29 16 21 6 15 14 10
+@1831_577_545_F3
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++
+29 29 27 27 24 30 27 29 30 32 27 19 23 16 31 27 31 23 28 28 31 22 21 14 21 16 27 24 20 13 20 24 23 23 12
+@1831_577_559_F3
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++
+13 27 31 26 30 30 31 29 31 30 14 17 27 13 31 16 28 29 16 17 28 21 16 14 26 28 30 13 5 17 10 24 17 8 6
+@1831_577_562_F3
+T32331101301233110121000220031120031
++
+2 7 7 5 9 5 15 4 8 16 4 8 2 7 3 17 12 11 9 9 9 4 14 12 11 11 8 8 5 11 12 13 16 6 9
+@1831_577_637_F3
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++
+23 12 11 19 2 29 25 12 21 10 25 23 11 5 7 20 26 18 28 15 29 22 28 21 23 5 16 14 24 5 6 30 26 19 11
+@1831_577_641_F3
+T13031301101121223221212020032131113
++
+5 19 22 26 14 6 25 32 26 26 20 30 25 22 17 11 7 28 8 11 2 9 30 10 13 2 5 22 3 23 2 4 22 14 6
+@1831_577_692_F3
+T01122320200330103121202301211100220
++
+31 33 11 31 30 31 33 7 31 32 30 31 10 31 31 29 31 10 30 28 29 31 6 28 27 31 27 28 27 24 28 30 22 20 27
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/combine_phiX_out_2.fastqcssanger	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,576 @@
+@1831_573_1004_F3
+T00030133312212111300011021310132222
++
+%><C&&9952+C>5<.?<79,=42<292:<(9/-7
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++
+);@@17?@=>7??@A8?==@4A?A4)&+.'&+'1,
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++
+.++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$
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++
+@@@=4/+)5)408?'665>*/5?<61';<3,:,5-
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++
+>>>::>17=A5?@@=;7A=;2.60>82<8=74+;;
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++
+)='@#%3=.>)/34*117,,/6-4+.9742456<)
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++
+CB@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+?
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++
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++
+@@@@?,@??@$><=>+%/*>*1,)?26&12'9%7.
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++
+(,//*,#8''.6''6'2&27/80)%&#0'%#*,2'
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++
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++
+=?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4
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++
+7>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>?
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++
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++
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++
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++
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++
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++
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++
+@<4;%%@7>#*>97%6;+8$#<07%1372$%<54#
+@1831_574_243_F3
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++
+#@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97
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++
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++
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++
+))$>/>8):2@:213;;.1)@3%64%+)<7)+$92
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++
+7?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/<
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++
+73-5)19,,<@>4067<2.-864346;9<1/;212
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++
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++
+9'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4
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++
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++
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++
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++
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++
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++
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++
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++
+:5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6
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++
+AA5A5B@5:;@@,.9?A1?#.?;3),>82%)='7*
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++
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++
+-?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/'
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++
+>7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1
+@1831_574_1560_F3
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++
+=))&65<4=>99@:597(1&;+&(%&4#,#&&&*$
+@1831_574_1591_F3
+T23202101330322130221230222201123202
++
+==<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9
+@1831_574_1624_F3
+T20122200222132200313011102302210332
++
+#<6.&(,7-+))7..'/;43.)927.(<85&13-)
+@1831_574_1826_F3
+T13012312120112021233030302313201111
++
++@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$
+@1831_574_1903_F3
+T30232100103132133321330310210101221
++
+<956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/
+@1831_574_1961_F3
+T02333101331223303300200011100032200
++
+6>-07-@>(2'@<#064@%5%@@6.&<<(9)=:47
+@1831_575_54_F3
+T13331330322230200102132110132013200
++
+>=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8
+@1831_575_80_F3
+T33133322233322221003332230323312313
++
+*?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6&
+@1831_575_192_F3
+T30013012111133003301010212123302011
++
+0:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7'
+@1831_575_197_F3
+T33312113010133020301131330001310032
++
+,-:?463@A:88?6?437<=.2&1.;@67.4@%2,
+@1831_575_223_F3
+T10121010002202131221210302100121020
++
+@?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&'
+@1831_575_420_F3
+T31110103220000101310112112001020212
++
+82?.>?(-''2+..@),$%1@;')1)?+)7.')..
+@1831_575_434_F3
+T30312132120223101113223301211113311
++
+<@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3)
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
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++
+(+'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#*
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++
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++
+@@46=@C.??<A79@@;-<@@>29B?>55<B7598
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++
+=@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,%
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++
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++
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++
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++
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++
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+@1831_576_882_F3
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++
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++
+=@@C2?C>?<>@886B?;?.??87=B<8<15??=.
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++
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++
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++
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++
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+@1831_576_1131_F3
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++
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+@1831_576_1168_F3
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++
+>@CC6@@2?9=>7?;76<;467@;9,0%26'',4$
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++
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+@1831_576_1289_F3
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++
+@9<>1B@@;7@@663==28,5':8<<,.=2>>.50
+@1831_576_1329_F3
+T01100302102020113003022000120002100
++
+<>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2
+@1831_576_1367_F3
+T12231310311233110031222013332011023
++
+??@@<>@@=@<@<=@>@??9:?<=>=<8;59@787
+@1831_576_1416_F3
+T33021233100123120313103133211203221
++
++';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@
+@1831_576_1461_F3
+T32022221221112233100210223002100100
++
+#1&74#(#(&##$#,'###%#%%#*#&%%##%%%'
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++
+6<@C@@>1;@:;<<@@9@???9<3?5-21=4877,
+@1831_576_1664_F3
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++
+@@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;)
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++
+@@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6%
+@1831_576_1729_F3
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++
+@?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=>
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++
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++
+,@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@
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++
+)##()(#&##)%)/-#%$11#%3>'##&$,#$$'+
+@1831_576_2014_F3
+T31123201010100321122111102113021003
++
+@@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1
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++
+5<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+
+@1831_577_40_F3
+T11111212330120012020200031313303003
++
+92/4('.')(<*?#$)%&<,/39<(.2,+<=@611
+@1831_577_119_F3
+T33111010021103320103213121313000102
++
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++
+/4@>>?=1?:+>@07@@><>@*<+1@15)96'2$)
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++
+7<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5#
+@1831_577_281_F3
+T03032301231212301013112222111210000
++
+7-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:?
+@1831_577_288_F3
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++
+5;/79??&=B::298*6.7/+4&21,7,6?.7#'6
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++
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++
+62B?:@?@<?958=,3:,90:&'-99,6<5.($+6
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++
+12957/:1))=76(*24;,3+:<.&.&-=1=2/5*
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++
+3=<7/<826)>#.'&4204+5#/041.7*91&756
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++
+:48.,*>6566<?8=<=<2>6;94>;=9>@8924@
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++
+#7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+
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+T00112131333222303222210031322103233
++
+>><<9?<>?A<481@<@8==@76/61<95.5988-
+@1831_577_559_F3
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++
+.<@;??@>@?/2<.@1=>12=61/;=?.&2+92)'
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++
+#((&*&0%)1%)#($2-,***%/-,,))&,-.1'*
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+T22113312122202103031023120301031110
++
+8-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4,
+@1831_577_641_F3
+T13031301101121223221212020032131113
++
+&47;/':A;;5?:72,(=),#*?+.#&7$8#%7/'
+@1831_577_692_F3
+T01122320200330103121202301211100220
++
+@B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75<
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_combiner_in_1.fasta	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,14 @@
+>SRR014849.50939 EIXKN4201BA2EC length=135
+GAAATTTCAGGGCCACCTTTTTTTT
+GATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGA
+GAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
+>SRR014849.110027 EIXKN4201APUB0 length=131
+CTTCAAATGATTC
+CGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCC
+TTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGAC
+CAGAACGATCCG
+>SRR014849.203935 EIXKN4201B4HU6 length=144
+AACCCGTCCCA
+TCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACC
+CCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTT
+TAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_combiner_in_1.qual454	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,22 @@
+>SRR014849.110027 EIXKN4201APUB0 length=131
+=B::@<':=5A9?7EA0:=<<?6@7<3?5<
+@;%D?-B=)::0=4<D?
+-EA/D@2";B;B:
+B:A9;;=<B;;<B;<B;<B;:A;<A;8FB7
++=<B;B:A9<1:=FB6(<=<<EA0956;<2
+==A8===:@8=
+>SRR014849.203935 EIXKN4201B4HU6 length=144
+A;@;%75?:#<<9EA1;=EA3%B;B;A;B;
+@;%9EA1EA1EA3%<B;A;8EA0D@
+3$EA1
+=B;A;B;B;:=:B;:B:A9:EA0A9<FA81
++&"D?-B;4<::/<;=:A98-5?6=C>+8<
+<3;=4:DA3%<;=8-9.A=):B=*
+>SRR014849.50939 EIXKN4201BA2EC length=135
+;C?-EA/=<EA/B;<B;D>60,)%"<=:5<
+@8<B;=B;<;E
+A4'@8FB6*<:=<<===<=
+;=B:A9<<B;=B;=EA0:<B:<<=<<FA81
++$?6;<A9=<3>5@7@8<A<(B=*A=)<<2
+?57B=*B=*D?-:=4
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_combiner_no_qual_ascii_out_1.fastqcssanger	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,576 @@
+@1831_573_1004_F3
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++
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++
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++
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+T31312310323301210002210123101021011
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+T10322001220012223202202222001230222
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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+T13310013212312012302121010221231123
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
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++
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++
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_combiner_no_qual_decimal_out_1.fastqsanger	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,12 @@
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++
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/s2fq_phiX.csfasta	Mon Jan 27 09:28:39 2014 -0500
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+20 27 29 24 29 20 6 17 7 5 22 15 22 13 23 2 5 5 18 24 11 15 4 22 14 2 7 2 11 9 4 5 20 9 10
+>1831_577_40_F3
+24 17 14 19 7 6 13 6 8 7 27 9 30 2 3 8 4 5 27 11 14 18 24 27 7 13 17 11 10 27 28 31 21 16 16
+>1831_577_119_F3
+24 29 30 34 16 16 8 12 16 14 8 2 26 2 14 11 23 20 15 9 10 13 10 3 3 20 20 20 15 10 4 12 13 19 15
+>1831_577_133_F3
+14 19 31 29 29 30 28 16 30 25 10 29 31 15 22 31 31 29 27 29 31 9 27 10 16 31 16 20 8 24 21 6 17 3 8
+>1831_577_255_F3
+22 27 28 23 22 31 29 21 24 4 9 9 2 5 2 12 10 3 13 2 5 5 2 10 3 12 10 4 5 4 13 11 4 20 2
+>1831_577_281_F3
+22 12 25 33 26 23 31 28 26 29 22 31 29 19 30 28 30 10 21 20 24 30 26 20 27 22 30 26 24 31 23 7 29 25 30
+>1831_577_288_F3
+20 26 14 22 24 30 30 5 28 33 25 25 17 24 23 9 21 13 22 14 10 19 5 17 16 11 22 11 21 30 13 22 2 6 21
+>1831_577_322_F3
+24 28 26 29 19 20 15 21 26 17 20 20 19 21 19 12 27 2 22 10 16 24 19 5 17 27 30 21 20 24 21 23 8 22 14
+>1831_577_362_F3
+21 17 33 30 25 31 30 31 27 30 24 20 23 28 11 18 25 11 24 15 25 5 6 12 24 24 11 21 27 20 13 7 3 10 21
+>1831_577_382_F3
+16 17 24 20 22 14 25 16 8 8 28 22 21 7 9 17 19 26 11 18 10 25 27 13 5 13 5 12 28 16 28 17 14 20 9
+>1831_577_464_F3
+18 28 27 22 14 27 23 17 21 8 29 2 13 6 5 19 17 15 19 10 20 2 14 15 19 16 13 22 9 24 16 5 22 20 21
+>1831_577_488_F3
+25 19 23 13 11 9 29 21 20 21 21 27 30 23 28 27 28 27 17 29 21 26 24 19 29 26 28 24 29 31 23 24 17 19 31
+>1831_577_511_F3
+2 22 14 10 5 3 25 27 22 4 21 11 3 3 4 6 4 14 10 8 2 3 22 7 7 5 9 18 29 16 21 6 15 14 10
+>1831_577_545_F3
+29 29 27 27 24 30 27 29 30 32 27 19 23 16 31 27 31 23 28 28 31 22 21 14 21 16 27 24 20 13 20 24 23 23 12
+>1831_577_559_F3
+13 27 31 26 30 30 31 29 31 30 14 17 27 13 31 16 28 29 16 17 28 21 16 14 26 28 30 13 5 17 10 24 17 8 6
+>1831_577_562_F3
+2 7 7 5 9 5 15 4 8 16 4 8 2 7 3 17 12 11 9 9 9 4 14 12 11 11 8 8 5 11 12 13 16 6 9
+>1831_577_637_F3
+23 12 11 19 2 29 25 12 21 10 25 23 11 5 7 20 26 18 28 15 29 22 28 21 23 5 16 14 24 5 6 30 26 19 11
+>1831_577_641_F3
+5 19 22 26 14 6 25 32 26 26 20 30 25 22 17 11 7 28 8 11 2 9 30 10 13 2 5 22 3 23 2 4 22 14 6
+>1831_577_692_F3
+31 33 11 31 30 31 33 7 31 32 30 31 10 31 31 29 31 10 30 28 29 31 6 28 27 31 27 28 27 24 28 30 22 20 27
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wrapping_as_sanger.fastqsanger	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,12 @@
+@SRR014849.50939 EIXKN4201BA2EC length=135
+GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
++
+;C?-EA/=<EA/B;<B;D>60,)%"<=:5<@8<B;=B;<;EA4'@8FB6*<:=<<===<=;=B:A9<<B;=B;=EA0:<B:<<=<<FA81+$?6;<A9=<3>5@7@8<A<(B=*A=)<<2?57B=*B=*D?-:=4
+@SRR014849.110027 EIXKN4201APUB0 length=131
+CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
++
+=B::@<':=5A9?7EA0:=<<?6@7<3?5<@;%D?-B=)::0=4<D?-EA/D@2";B;B:B:A9;;=<B;;<B;<B;<B;:A;<A;8FB7+=<B;B:A9<1:=FB6(<=<<EA0956;<2==A8===:@8=
+@SRR014849.203935 EIXKN4201B4HU6 length=144
+AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
++
+A;@;%75?:#<<9EA1;=EA3%B;B;A;B;@;%9EA1EA1EA3%<B;A;8EA0D@3$EA1=B;A;B;B;:=:B;:B:A9:EA0A9<FA81+&"D?-B;4<::/<;=:A98-5?6=C>+8<<3;=4:DA3%<;=8-9.A=):B=*
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wrapping_as_sanger_decimal.fastqsanger	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,12 @@
+@SRR014849.50939 EIXKN4201BA2EC length=135
+GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
++
+26 34 30 12 36 32 14 28 27 36 32 14 33 26 27 33 26 35 29 21 15 11 8 4 1 27 28 25 20 27 31 23 27 33 26 28 33 26 27 26 36 32 19 6 31 23 37 33 21 9 27 25 28 27 27 28 28 28 27 28 26 28 33 25 32 24 27 27 33 26 28 33 26 28 36 32 15 25 27 33 25 27 27 28 27 27 37 32 23 16 10 3 30 21 26 27 32 24 28 27 18 29 20 31 22 31 23 27 32 27 7 33 28 9 32 28 8 27 27 17 30 20 22 33 28 9 33 28 9 35 30 12 25 28 19
+@SRR014849.110027 EIXKN4201APUB0 length=131
+CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
++
+28 33 25 25 31 27 6 25 28 20 32 24 30 22 36 32 15 25 28 27 27 30 21 31 22 27 18 30 20 27 31 26 4 35 30 12 33 28 8 25 25 15 28 19 27 35 30 12 36 32 14 35 31 17 1 26 33 26 33 25 33 25 32 24 26 26 28 27 33 26 26 27 33 26 27 33 26 27 33 26 25 32 26 27 32 26 23 37 33 22 10 28 27 33 26 33 25 32 24 27 16 25 28 37 33 21 7 27 28 27 27 36 32 15 24 20 21 26 27 17 28 28 32 23 28 28 28 25 31 23 28
+@SRR014849.203935 EIXKN4201B4HU6 length=144
+AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
++
+32 26 31 26 4 22 20 30 25 2 27 27 24 36 32 16 26 28 36 32 18 4 33 26 33 26 32 26 33 26 31 26 4 24 36 32 16 36 32 16 36 32 18 4 27 33 26 32 26 23 36 32 15 35 31 18 3 36 32 16 28 33 26 32 26 33 26 33 26 25 28 25 33 26 25 33 25 32 24 25 36 32 15 32 24 27 37 32 23 16 10 5 1 35 30 12 33 26 19 27 25 25 14 27 26 28 25 32 24 23 12 20 30 21 28 34 29 10 23 27 27 18 26 28 19 25 35 32 18 4 27 26 28 23 12 24 13 32 28 8 25 33 28 9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jan 27 09:28:39 2014 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="galaxy_sequence_utils" version="1.0.0">
+      <repository changeset_revision="0643676ad5f7" name="package_galaxy_utils_1_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>