# HG changeset patch
# User lparsons
# Date 1445542857 14400
# Node ID 80e84db1c3927e12203b48a2a71f228314139f0f
# Parent  d1a0e620185411c6b95b36bdb49dbc32f2f4408d
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 9ece31c748369db47d9817066cb91e6f3e8428c8-dirty

diff -r d1a0e6201854 -r 80e84db1c392 fastx_barcode_splitter.xml
--- a/fastx_barcode_splitter.xml	Thu Nov 07 17:18:51 2013 -0500
+++ b/fastx_barcode_splitter.xml	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 fastx_barcode_splitter_galaxy_wrapper.sh
--- a/fastx_barcode_splitter_galaxy_wrapper.sh	Thu Nov 07 17:18:51 2013 -0500
+++ b/fastx_barcode_splitter_galaxy_wrapper.sh	Thu Oct 22 15:40:57 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 -i -e '$_ =~ s|\t|</td><td>|g; print "<tr><td>\n$_</td></tr>\n"'
 echo "<p>"
 echo "</table></body></html>"
diff -r d1a0e6201854 -r 80e84db1c392 test-data/fastx_barcode_splitter1.out
--- a/test-data/fastx_barcode_splitter1.out	Thu Nov 07 17:18:51 2013 -0500
+++ b/test-data/fastx_barcode_splitter1.out	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 testoutput/fastx_barcode_splitter1.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testoutput/fastx_barcode_splitter1.out	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/BC1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/BC1	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/BC2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/BC2	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/BC3
diff -r d1a0e6201854 -r 80e84db1c392 tmp/BC4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/BC4	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/tmp_BC1_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC1_visible.fastqsanger	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/tmp_BC1_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC1_visible_fastqsanger	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/tmp_BC2_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC2_visible.fastqsanger	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/tmp_BC2_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC2_visible_fastqsanger	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/tmp_BC3_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC3_visible.fastqsanger	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/tmp_BC3_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC3_visible_fastqsanger	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/tmp_BC4_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC4_visible.fastqsanger	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/tmp_BC4_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC4_visible_fastqsanger	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/tmp_unmatched_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_unmatched_visible.fastqsanger	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/tmp_unmatched_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_unmatched_visible_fastqsanger	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp/unmatched
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/unmatched	Thu Oct 22 15:40:57 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 d1a0e6201854 -r 80e84db1c392 tmp_stdio.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp_stdio.txt	Thu Oct 22 15:40:57 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