# HG changeset patch
# User lparsons
# Date 1445960872 14400
# Node ID b7b3d008e2d33fa81db7bf7e08b63b74571c830f
# Parent  84bbf4fd24c3c05620a6454221f0ee33f938028d
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit e6a486662201362134119c0ddc7151b8dd181ebd

diff -r 84bbf4fd24c3 -r b7b3d008e2d3 fastx_barcode_splitter.xml
--- a/fastx_barcode_splitter.xml	Fri Nov 08 09:53:39 2013 -0500
+++ b/fastx_barcode_splitter.xml	Tue Oct 27 11:47:52 2015 -0400
@@ -1,59 +1,60 @@
 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter" force_history_refresh="True">
 	<description></description>
-	<command interpreter="bash">
-		fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $input.extension --mismatches $mismatches --partial $partial 
-		#if $refBarcodeLocation.barcodeLocation == "idxfile":
-		  --idxfile $refBarcodeLocation.idxfile 
-		#else: 
-		  $refBarcodeLocation.EOL 
-		#end if
-		> $output
+	<command interpreter="bash"><![CDATA[
+fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $input.extension --mismatches $mismatches --partial $partial
+#if $refBarcodeLocation.barcodeLocation == "idxfile":
+    --idxfile $refBarcodeLocation.idxfile
+#else:
+    $refBarcodeLocation.EOL
+#end if
+> $output
+]]>
 	</command>
 
 	<inputs>
-		<param format="txt" version="1.1" name="BARCODE" type="data" label="Barcodes to use" />
-		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" version="1.1" name="input" type="data" label="Library to split" />
+		<param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
+		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
 
 		<conditional name="refBarcodeLocation">
-			<param version="1.1" name="barcodeLocation" type="select" label="Barcodes found at">
+			<param name="barcodeLocation" type="select" label="Barcodes found at">
 				<option value="bol">Start of sequence (5' end)</option>
 				<option value="eol">End of sequence (3' end)</option>
 				<option value="idxfile">Separate index file</option>
 			</param>
 			<when value="bol">
-				<param version="1.1" name="EOL" type="hidden" value="--bol" />
+				<param name="EOL" type="hidden" value="--bol" />
 			</when>
 			<when value="eol">
-				<param version="1.1" name="EOL" type="hidden" value="--eol" />
+				<param name="EOL" type="hidden" value="--eol" />
 			</when>
 			<when value="idxfile">
-				<param version="1.1" name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
+				<param name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
 			</when>
 		</conditional>
 
-		<param version="1.1" name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
-		
-		<param version="1.1" name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
-	
+		<param name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
+
+		<param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
+
 	</inputs>
-	
-	<tests>
+
+	<outputs>
+		<data format="html" name="output" />
+	</outputs>
+
+    <tests>
 		<test>
 			<!-- Split a FASTQ file -->
-			<param version="1.1" name="BARCODE" value="fastx_barcode_splitter1.txt" />
-			<param version="1.1" name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
-			<param version="1.1" name="EOL" value="Start of sequence (5' end)" />
-			<param version="1.1" name="mismatches" value="2" />
-			<param version="1.1" name="partial" value="0" />
-			<output version="1.1" name="output" file="fastx_barcode_splitter1.out" />
+			<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+			<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
+			<param name="barcodeLocation" value="bol" />
+			<param name="mismatches" value="2" />
+			<param name="partial" value="0" />
+			<output name="output" file="fastx_barcode_splitter1.out" />
 		</test>
 	</tests>
 
-	<outputs>
-		<data version="1.1" format="html" name="output" />
-	</outputs>
-<help>
-
+    <help><![CDATA[
 **What it does**
 
 This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria.
@@ -71,7 +72,7 @@
     BC2	ATCGT
     BC3	GTGAT
     BC4 TGTCT
-    
+
 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
 Sequences matching the barcode will be stored in the appropriate file.
 
@@ -79,14 +80,18 @@
 
 The output of this tool is an HTML file, displaying the split counts and the file names.
 In addition, each fastq file produced will be loaded into the galaxy history automatically.
-
-
-------
-
-This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+]]>
+	</help>
 
- .. __: http://hannonlab.cshl.edu/fastx_toolkit/
- 
-</help>
-<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+	<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+	<citations>
+	    <citation type="bibtex">
+			@misc{gordon_fastx-toolkit_????,
+				title = {{FASTX}-{Toolkit}},
+				url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
+				author = {Gordon, Assaf}
+			}
+		</citation>
+	</citations>
+
 </tool>
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 fastx_barcode_splitter_galaxy_wrapper.sh
--- a/fastx_barcode_splitter_galaxy_wrapper.sh	Fri Nov 08 09:53:39 2013 -0500
+++ b/fastx_barcode_splitter_galaxy_wrapper.sh	Tue Oct 27 11:47:52 2015 -0400
@@ -18,11 +18,12 @@
 
 #  Modified by Lance Parsons (lparsons@princeton.edu)
 #	2011-03-15	Adapted to allow galaxy to determine filetype
+#	2015-10-21	Updated to make compatible with OSX (BSD sed)
 #
 #This is a shell script wrapper for 'fastx_barcode_splitter.pl'
 #
 # 1. Output files are saved at the dataset's files_path directory.
-#    
+#
 # 2. 'fastx_barcode_splitter.pl' outputs a textual table.
 #    This script turns it into pretty HTML with working URL
 #    (so lazy users can just click on the URLs and get their files)
@@ -68,7 +69,7 @@
 BASEPATH="$OUTPUT_PATH/"
 #PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__"
 PREFIX="$BASEPATH""${LIBNAME}_"
-SUFFIX="_visible_$FILETYPE"
+SUFFIX="_visible.$FILETYPE"
 DIRECTORY=$(cd `dirname $0` && pwd)
 
 RESULTS=`gzip -cdf "$FASTQ_FILE" | $DIRECTORY/fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"`
@@ -80,11 +81,8 @@
 # Convert the textual tab-separated table into simple HTML table,
 # with the local path replaces with a valid URL
 #HTMLSUMMARY=${PREFIX}stats_visible_html
-echo "<html><body><table border=1>" 
-echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|\\1|" | sed '
-i<tr><td>
-s|\t|</td><td>|g
-a<\/td><\/tr>
-'
+echo "<html><body><table border=1>"
+echo "$RESULTS" | sed "s|$BASEPATH\\(.*\\)|<a href=\"\\1\">\\1</a>|" | \
+perl -n -e '$_ =~ s|\t|</td><td>|g; print "<tr><td>\n$_</td></tr>\n"'
 echo "<p>"
 echo "</table></body></html>"
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 test-data/fastx_barcode_splitter1.out
--- a/test-data/fastx_barcode_splitter1.out	Fri Nov 08 09:53:39 2013 -0500
+++ b/test-data/fastx_barcode_splitter1.out	Tue Oct 27 11:47:52 2015 -0400
@@ -3,19 +3,19 @@
 Barcode</td><td>Count</td><td>Location
 </td></tr>
 <tr><td>
-BC1</td><td>11</td><td><a href="fastx_barcode_splitter1_fastq__BC1.txt">fastx_barcode_splitter1_fastq__BC1.txt</a>
+BC1</td><td>11</td><td><a href="primary_3_BC1_visible.fastqsolexa">primary_3_BC1_visible.fastqsolexa</a>
 </td></tr>
 <tr><td>
-BC2</td><td>12</td><td><a href="fastx_barcode_splitter1_fastq__BC2.txt">fastx_barcode_splitter1_fastq__BC2.txt</a>
+BC2</td><td>12</td><td><a href="primary_3_BC2_visible.fastqsolexa">primary_3_BC2_visible.fastqsolexa</a>
 </td></tr>
 <tr><td>
-BC3</td><td>9</td><td><a href="fastx_barcode_splitter1_fastq__BC3.txt">fastx_barcode_splitter1_fastq__BC3.txt</a>
+BC3</td><td>9</td><td><a href="primary_3_BC3_visible.fastqsolexa">primary_3_BC3_visible.fastqsolexa</a>
 </td></tr>
 <tr><td>
-BC4</td><td>1</td><td><a href="fastx_barcode_splitter1_fastq__BC4.txt">fastx_barcode_splitter1_fastq__BC4.txt</a>
+BC4</td><td>1</td><td><a href="primary_3_BC4_visible.fastqsolexa">primary_3_BC4_visible.fastqsolexa</a>
 </td></tr>
 <tr><td>
-unmatched</td><td>9</td><td><a href="fastx_barcode_splitter1_fastq__unmatched.txt">fastx_barcode_splitter1_fastq__unmatched.txt</a>
+unmatched</td><td>9</td><td><a href="primary_3_unmatched_visible.fastqsolexa">primary_3_unmatched_visible.fastqsolexa</a>
 </td></tr>
 <tr><td>
 total</td><td>42
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 testoutput/fastx_barcode_splitter1.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testoutput/fastx_barcode_splitter1.out	Tue Oct 27 11:47:52 2015 -0400
@@ -0,0 +1,24 @@
+<html><body><table border=1>
+<tr><td>
+Barcode</td><td>Count</td><td>Location
+</td></tr>
+<tr><td>
+BC1</td><td>11</td><td><a href="primary_3_BC1_visible_fastqsolexa">primary_3_BC1_visible_fastqsolexa<a>
+</td></tr>
+<tr><td>
+BC2</td><td>12</td><td><a href="primary_3_BC2_visible_fastqsolexa">primary_3_BC2_visible_fastqsolexa<a>
+</td></tr>
+<tr><td>
+BC3</td><td>9</td><td><a href="primary_3_BC3_visible_fastqsolexa">primary_3_BC3_visible_fastqsolexa<a>
+</td></tr>
+<tr><td>
+BC4</td><td>1</td><td><a href="primary_3_BC4_visible_fastqsolexa">primary_3_BC4_visible_fastqsolexa<a>
+</td></tr>
+<tr><td>
+unmatched</td><td>9</td><td><a href="primary_3_unmatched_visible_fastqsolexa">primary_3_unmatched_visible_fastqsolexa<a>
+</td></tr>
+<tr><td>
+total</td><td>42
+</td></tr>
+<p>
+</table></body></html>
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 tmp/BC1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/BC1	Tue Oct 27 11:47:52 2015 -0400
@@ -0,0 +1,32 @@
+@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
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 tmp/BC2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/BC2	Tue Oct 27 11:47:52 2015 -0400
@@ -0,0 +1,32 @@
+@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
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 tmp/BC3
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 tmp/BC4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/BC4	Tue Oct 27 11:47:52 2015 -0400
@@ -0,0 +1,4 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TGTCTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
\ No newline at end of file
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 tmp/tmp_BC1_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC1_visible.fastqsanger	Tue Oct 27 11:47:52 2015 -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 84bbf4fd24c3 -r b7b3d008e2d3 tmp/tmp_BC1_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC1_visible_fastqsanger	Tue Oct 27 11:47:52 2015 -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 84bbf4fd24c3 -r b7b3d008e2d3 tmp/tmp_BC2_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC2_visible.fastqsanger	Tue Oct 27 11:47:52 2015 -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 84bbf4fd24c3 -r b7b3d008e2d3 tmp/tmp_BC2_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC2_visible_fastqsanger	Tue Oct 27 11:47:52 2015 -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 84bbf4fd24c3 -r b7b3d008e2d3 tmp/tmp_BC3_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC3_visible.fastqsanger	Tue Oct 27 11:47:52 2015 -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 84bbf4fd24c3 -r b7b3d008e2d3 tmp/tmp_BC3_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC3_visible_fastqsanger	Tue Oct 27 11:47:52 2015 -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 84bbf4fd24c3 -r b7b3d008e2d3 tmp/tmp_BC4_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC4_visible.fastqsanger	Tue Oct 27 11:47:52 2015 -0400
@@ -0,0 +1,4 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TGTCTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
\ No newline at end of file
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 tmp/tmp_BC4_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC4_visible_fastqsanger	Tue Oct 27 11:47:52 2015 -0400
@@ -0,0 +1,4 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TGTCTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
\ No newline at end of file
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 tmp/tmp_unmatched_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_unmatched_visible.fastqsanger	Tue Oct 27 11:47:52 2015 -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
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 tmp/tmp_unmatched_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_unmatched_visible_fastqsanger	Tue Oct 27 11:47:52 2015 -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
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 tmp/unmatched
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/unmatched	Tue Oct 27 11:47:52 2015 -0400
@@ -0,0 +1,100 @@
+@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
+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
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff -r 84bbf4fd24c3 -r b7b3d008e2d3 tmp_stdio.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp_stdio.txt	Tue Oct 27 11:47:52 2015 -0400
@@ -0,0 +1,7 @@
+Barcode	Count	Location
+BC1	8	tmp/BC1
+BC2	8	tmp/BC2
+BC3	0	tmp/BC3
+BC4	1	tmp/BC4
+unmatched	25	tmp/unmatched
+total	42