# HG changeset patch
# User hepcat72
# Date 1473270491 14400
# Node ID 5e0fd61660b7a35408707c3f87d9528159dfeb40
# Parent  e3f91eee8c7521add38d113332e00ee6c80b6af9
Streamlined the galaxy interface by removing the parameter to indicate the number of columns in the barcode file.  Separated the index file inputs from the read file inputs.  Restricted the number of allowed mismatches to 2.

diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/._barcode_splitter.py
Binary file barcode_splitter_multi/._barcode_splitter.py has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/barcode_splitter.py
--- a/barcode_splitter_multi/barcode_splitter.py	Mon Aug 29 15:21:20 2016 -0400
+++ b/barcode_splitter_multi/barcode_splitter.py	Wed Sep 07 13:48:11 2016 -0400
@@ -10,7 +10,7 @@
 from collections import defaultdict
 import subprocess
 
-__version__      = "0.13"
+__version__      = "0.14"
 __author__       = "Lance Parsons & Robert Leach"
 __author_email__ = "lparsons@princeton.edu,rleach@princeton.edu"
 __copyright__    = "Copyright 2011, Lance Parsons & Robert leach"
@@ -52,12 +52,6 @@
                                 'of the index read (default is at the '
                                 'beginning)')
 
-    #pairedend_group = parser.add_argument_group("Paired-End")
-    #pairedend_group.add_argument ('--split-paired-ends', action='store_true',
-    #                              default=False, help='In addition to '
-    #                              'splitting based on barcodes, also split '
-    #                              'paired ends.')
-
     output_group = parser.add_argument_group("Output Options")
     output_group.add_argument('--prefix', default='',
                               help='Prefix for output files')
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/barcode_splitter.xml
--- a/barcode_splitter_multi/barcode_splitter.xml	Mon Aug 29 15:21:20 2016 -0400
+++ b/barcode_splitter_multi/barcode_splitter.xml	Wed Sep 07 13:48:11 2016 -0400
@@ -1,18 +1,27 @@
-<tool id="cshl_princeton_fastx_barcode_splitter" version="0.4" name="Barcode Splitter">
+<tool id="cshl_princeton_fastx_barcode_splitter" version="0.13" name="Barcode Splitter">
   <description></description>
   <command interpreter="bash" detect_errors="aggressive"><![CDATA[
 barcode_splitter_galaxy_wrapper.sh split
-#for $sf in $seqfiles
-    ${sf.input.extension}
+##There must be an index file, so supply the extension of the first one
+#for $indf in $indexfiles
+    ${indf.input2.extension}
     #break
 #end for
---bcfile $bcfile --mismatches $mismatches --galaxy $zip $barcodes_at_end
-#for $sf in $seqfiles
-    ${sf.input}
-#end for
+--bcfile $bcfile --mismatches $mismatches --galaxy $barcodes_at_end
+#set $num_index_files = 1
+#if self.varExists('indexfiles'):
+    #for $indf in $indexfiles
+        ${indf.input2}
+        #set $num_index_files += 1
+    #end for
+#end if
+#if self.varExists('seqfiles'):
+    #for $sf in $seqfiles
+        ${sf.input}
+    #end for
+#end if
 --idxread
-#set $bound = $num_barcode_columns.value + 1
-#for $n in range( 1, $bound )
+#for $n in range( 1, $num_index_files )
     ${n}
 #end for
 > $summary
@@ -21,20 +30,18 @@
 
   <inputs>
     <param format="txt" name="bcfile" type="data" label="Barcode File" help="Tab-delimited text file where the first column is a sample ID and subsequent columns are barcodes." />
-    <param name="num_barcode_columns" type="integer" size="2" value="1" label="Number of barcode columns" help="The number of columns in the barcode file containing barcode sequences.  Note that you must submit at least this many read files." />
 
 
-    <repeat name="seqfiles" title="Read Files" min="1" default="2">
-        <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" help="Barcoded reads files must be first. If there are multiple barcode columns in the barcode file, the files must be supplied in the same order as the barcode columns (from left to right)." />
+    <repeat name="seqfiles" title="Read Files" min="0" default="1">
+        <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Typically 'Read 1'" help="If your reads file has barcodes embedded in it, do not enter it here - use the 'Index Files' field below." />
+    </repeat>
+    <repeat name="indexfiles" title="Index Files" min="0" default="1">
+        <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="input2" type="data" label="Typically 'Read 2 (Index Read)'" help="If there are multiple barcode columns in the barcode file, the files must be supplied in the same order as the barcode columns (from left to right).  There must be as many index files as there are barcode columns in the barcodes file.  If your reads have barcodes embedded in them (at the beginning or end), that file must be submitted here as an index file." />
     </repeat>
 
-    <param name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
+    <param name="mismatches" type="integer" size="3" value="0" max="2" min="0" label="Number of allowed mismatches" help="An integer between 0 and 2 (inclusive).  Warning: Make sure your barcodes all differ from one another by at least this many nucleotides plus 1, otherwise sequences that match both barcodes equally well will be thrown out as 'multimatched' reads." />
 
-    <param name="barcodes_at_end" type="boolean" truevalue="--barcodes_at_end" falsevalue="" checked="false"
-        label="Barcodes are at the end of all sequences" help="Default is the beginning of all sequences" />
-
-    <param name="zip" type="boolean" truevalue="--gzip" falsevalue="" checked="false"
-        label="Compress/zip the output" help="This generates reads files with a .gz extension.  Default is based on the file extension of the first input file." />
+    <param name="barcodes_at_end" type="boolean" truevalue="--barcodes_at_end" falsevalue="" checked="false" label="Barcodes are at the end of all sequences" help="Default is the beginning of all sequences" />
 
   </inputs>
 
@@ -50,8 +57,8 @@
       <!-- Split a FASTQ file -->
       <param name="bcfile" value="barcode_splitter1.txt" />
       <param name="num_barcode_columns" value="1" />
-      <repeat name="seqfiles">
-        <param name="input" value="barcode_splitter1.fastq" ftype="fastqsolexa" />
+      <repeat name="indexfiles">
+        <param name="input2" value="barcode_splitter1.fastq" ftype="fastqsolexa" />
       </repeat>
       <param name="barcodes_at_end" value="" />
       <param name="mismatches" value="2" />
@@ -69,8 +76,8 @@
       <!-- Split a FASTQ file, using separate index read -->
       <param name="bcfile" value="barcode_splitter1.txt" />
       <param name="num_barcode_columns" value="1" />
-      <repeat name="seqfiles">
-        <param name="input" value="barcode_splitter_index.fastq" ftype="fastqsolexa" />
+      <repeat name="indexfiles">
+        <param name="input2" value="barcode_splitter_index.fastq" ftype="fastqsolexa" />
       </repeat>
       <repeat name="seqfiles">
         <param name="input" value="barcode_splitter1.fastq" ftype="fastqsolexa" />
@@ -110,9 +117,9 @@
 For each barcode, a new FASTQ file will be created (with the barcodes' identifier as part of the file name).
 Sequences matching the barcodes in a row will be stored in the appropriate file.
 
-The first sequence file submitted must contain sequences with the barcodes in the first column of the barcode file.  The second sequence file must contain sequences with the barcodes in the second column, and so on.  The 'Number of barcode columns' specified must match the number of actual columns in the barcode file.
+The first sequence file submitted must contain sequences with the barcodes in the first column of the barcode file.  The second sequence file must contain sequences with the barcodes in the second column, and so on.  The Number of Index Files supplied must match the number of actual columns in the barcode file and the order in which they are supplied must match the order of the barcode columns as well.
 
-One (possibly two) additional FASTQ files will be created: the 'unmatched' file (and the 'multimatched' file), where sequences not matching any barcode (or matching more than 1 barcode when mismatches are taken into account) will be stored.
+As many as 2 additional FASTQ output files will be created for each read/index file: the 'unmatched' file and the 'multimatched' file, where sequences not matching any barcode or matching more than 1 barcode (when mismatches are taken into account) will be stored.
 
 The output of this tool is a summary table displaying the split counts for each barcode identifier and the percentage of the total reads those represent.
 In addition, each fastq file produced will be loaded into the galaxy history as part of a collection list.
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/._barcode_splitter1.out
Binary file barcode_splitter_multi/test-data/._barcode_splitter1.out has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC1-read-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/BC1-read-1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,20 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC1-read-1.fastq.gz
Binary file barcode_splitter_multi/test-data/BC1-read-1.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC1-read-2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/BC1-read-2.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,20 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC1-read-2.fastq.gz
Binary file barcode_splitter_multi/test-data/BC1-read-2.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC2-read-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/BC2-read-1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,48 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC2-read-1.fastq.gz
Binary file barcode_splitter_multi/test-data/BC2-read-1.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC2-read-2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/BC2-read-2.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,48 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC2-read-2.fastq.gz
Binary file barcode_splitter_multi/test-data/BC2-read-2.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC3-read-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/BC3-read-1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC3-read-1.fastq.gz
Binary file barcode_splitter_multi/test-data/BC3-read-1.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC3-read-2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/BC3-read-2.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC3-read-2.fastq.gz
Binary file barcode_splitter_multi/test-data/BC3-read-2.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC4-read-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/BC4-read-1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,4 @@
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0:
+TGTCT
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0:
+aab^V
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC4-read-1.fastq.gz
Binary file barcode_splitter_multi/test-data/BC4-read-1.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC4-read-2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/BC4-read-2.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,4 @@
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+TGTCTGAGTATACACAT
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/BC4-read-2.fastq.gz
Binary file barcode_splitter_multi/test-data/BC4-read-2.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/barcode_splitter1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/barcode_splitter1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,168 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203/1
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203/1
+aab^V^aU]`aa^aZaa
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+TGTCTGAGTATACACAT
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/barcode_splitter1.fastq.gz
Binary file barcode_splitter_multi/test-data/barcode_splitter1.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/barcode_splitter1.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/barcode_splitter1.out	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,7 @@
+Sample	Barcode1	Count	Percent
+BC1	GATCT	5	11.90%
+BC2	ATCGT	12	28.57%
+BC3	GTGAT	9	21.43%
+BC4	TGTCT	1	2.38%
+multimatched	multimatched	6	14.29%
+unmatched	unmatched	9	21.43%
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/barcode_splitter1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/barcode_splitter1.txt	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,4 @@
+BC1	GATCT
+BC2	ATCGT
+BC3	GTGAT
+BC4	TGTCT
\ No newline at end of file
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/barcode_splitter1_BC1.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/barcode_splitter1_BC1.out	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,44 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/barcode_splitter1_BC2.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/barcode_splitter1_BC2.out	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,48 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/barcode_splitter1_BC3.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/barcode_splitter1_BC3.out	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/barcode_splitter1_BC4.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/barcode_splitter1_BC4.out	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,4 @@
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+TGTCTGAGTATACACAT
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/barcode_splitter1_unmatched.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/barcode_splitter1_unmatched.out	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203/1
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203/1
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/barcode_splitter_index.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/barcode_splitter_index.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,168 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203/2
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203/2
+aab^V
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0:
+TGTCT
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0:
+aab^V
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/multimatched-read-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/multimatched-read-1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,24 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/multimatched-read-1.fastq.gz
Binary file barcode_splitter_multi/test-data/multimatched-read-1.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/multimatched-read-2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/multimatched-read-2.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,24 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/multimatched-read-2.fastq.gz
Binary file barcode_splitter_multi/test-data/multimatched-read-2.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/testBC1-read-1.fastq
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/testBC2-read-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/testBC2-read-1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,48 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/testBC3-read-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/testBC3-read-1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/testBC4-read-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/testBC4-read-1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,4 @@
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+TGTCTGAGTATACACAT
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/testmultimatched-read-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/testmultimatched-read-1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,80 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203/1
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203/1
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/testunmatched-read-1.fastq
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/unmatched-read-1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/unmatched-read-1.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203/2
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203/2
+aab^V
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/unmatched-read-1.fastq.gz
Binary file barcode_splitter_multi/test-data/unmatched-read-1.fastq.gz has changed
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/unmatched-read-2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_splitter_multi/test-data/unmatched-read-2.fastq	Wed Sep 07 13:48:11 2016 -0400
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203/1
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203/1
+aab^V^aU]`aa^aZaa
diff -r e3f91eee8c75 -r 5e0fd61660b7 barcode_splitter_multi/test-data/unmatched-read-2.fastq.gz
Binary file barcode_splitter_multi/test-data/unmatched-read-2.fastq.gz has changed