# HG changeset patch
# User lparsons
# Date 1457735071 18000
# Node ID e7b7cdc1834de3c92e00bf4cac4cb706a688a8b3
# Parent  32304398ef671252c1cfbfc4caf784c0f000dd97
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit a3b5b09c69f880529df96bdd5e050d712fa35cf4-dirty

diff -r 32304398ef67 -r e7b7cdc1834d fastx_barcode_splitter.pl
--- a/fastx_barcode_splitter.pl	Fri Nov 13 12:43:14 2015 -0500
+++ b/fastx_barcode_splitter.pl	Fri Mar 11 17:24:31 2016 -0500
@@ -316,7 +316,7 @@
 	my $read_id = shift;
 	my $stripped_read_id = $read_id;
 	if ($read_id_check_strip_characters) {
-		if ($read_id =~ /@([a-zA-Z0-9_-]+):([0-9]+):([a-zA-Z0-9]+):([0-9]+):([0-9]+):([0-9]+):([0-9]+) ([0-9]+):([YN]):([0-9]+):([ACGT]+){0,1}/) { # CASAVA 1.8+
+		if ($read_id =~ /@([^:]+):([0-9]+):([^:]+):([0-9]+):([0-9]+):([0-9]+):([0-9]+) ([0-9]+):([YN]):([0-9]+):([ACGT]+){0,1}/) { # CASAVA 1.8+
 			my @parts = split(/ /,$read_id);
 			$stripped_read_id = $parts[0];
 		} else { # CASAVA 1.7 and earlier
diff -r 32304398ef67 -r e7b7cdc1834d fastx_barcode_splitter.xml
--- a/fastx_barcode_splitter.xml	Fri Nov 13 12:43:14 2015 -0500
+++ b/fastx_barcode_splitter.xml	Fri Mar 11 17:24:31 2016 -0500
@@ -60,6 +60,22 @@
                 <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
             </output>
 		</test>
+		<test>
+			<!-- Split a FASTQ file, using separate index read -->
+			<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+			<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
+			<param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" />
+			<param name="barcodeLocation" value="idxfile" />
+			<param name="mismatches" value="2" />
+			<param name="partial" value="0" />
+            <output name="output" file="fastx_barcode_splitter1.out">
+                <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
+                <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
+                <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
+                <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
+                <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
+            </output>
+		</test>
 	</tests>
 
     <help><![CDATA[
diff -r 32304398ef67 -r e7b7cdc1834d test-data/.fastx_barcode_splitter1.out.swp
Binary file test-data/.fastx_barcode_splitter1.out.swp has changed
diff -r 32304398ef67 -r e7b7cdc1834d test-data/.fastx_barcode_splitter1_BC4.out.swp
Binary file test-data/.fastx_barcode_splitter1_BC4.out.swp has changed
diff -r 32304398ef67 -r e7b7cdc1834d test-data/fastx_barcode_splitter1.fastq
--- a/test-data/fastx_barcode_splitter1.fastq	Fri Nov 13 12:43:14 2015 -0500
+++ b/test-data/fastx_barcode_splitter1.fastq	Fri Mar 11 17:24:31 2016 -0500
@@ -158,11 +158,11 @@
 TAGTTGAGTATACACAT
 +CSHL_3_FC042AGLLWW:1:2:7:203
 aab^V^aU]`aa^aZaa
-@CSHL_3_FC042AGLLWW:1:2:7:203
+@CSHL_3_FC042AGLLWW:1:2:7:203/1
 TAGTTTCTCTATGTACA
-+CSHL_3_FC042AGLLWW:1:2:7:203
++CSHL_3_FC042AGLLWW:1:2:7:203/1
 aab^V^aU]`aa^aZaa
-@CSHL_3_FC042AGLLWW:1:2:7:203
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
 TGTCTGAGTATACACAT
-+CSHL_3_FC042AGLLWW:1:2:7:203
-aab^V^aU]`aa^aZaa
\ No newline at end of file
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+aab^V^aU]`aa^aZaa
diff -r 32304398ef67 -r e7b7cdc1834d test-data/fastx_barcode_splitter1_BC4.out
--- a/test-data/fastx_barcode_splitter1_BC4.out	Fri Nov 13 12:43:14 2015 -0500
+++ b/test-data/fastx_barcode_splitter1_BC4.out	Fri Mar 11 17:24:31 2016 -0500
@@ -1,4 +1,4 @@
-@CSHL_3_FC042AGLLWW:1:2:7:203
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
 TGTCTGAGTATACACAT
-+CSHL_3_FC042AGLLWW:1:2:7:203
-aab^V^aU]`aa^aZaa
\ No newline at end of file
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+aab^V^aU]`aa^aZaa
diff -r 32304398ef67 -r e7b7cdc1834d test-data/fastx_barcode_splitter1_unmatched.out
--- a/test-data/fastx_barcode_splitter1_unmatched.out	Fri Nov 13 12:43:14 2015 -0500
+++ b/test-data/fastx_barcode_splitter1_unmatched.out	Fri Mar 11 17:24:31 2016 -0500
@@ -30,7 +30,7 @@
 TAGTTGAGTATACACAT
 +CSHL_3_FC042AGLLWW:1:2:7:203
 aab^V^aU]`aa^aZaa
-@CSHL_3_FC042AGLLWW:1:2:7:203
+@CSHL_3_FC042AGLLWW:1:2:7:203/1
 TAGTTTCTCTATGTACA
-+CSHL_3_FC042AGLLWW:1:2:7:203
++CSHL_3_FC042AGLLWW:1:2:7:203/1
 aab^V^aU]`aa^aZaa
diff -r 32304398ef67 -r e7b7cdc1834d test-data/fastx_barcode_splitter_index.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastx_barcode_splitter_index.fastq	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d testoutput/fastx_barcode_splitter1.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testoutput/fastx_barcode_splitter1.out	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/BC1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/BC1	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/BC2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/BC2	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/BC3
diff -r 32304398ef67 -r e7b7cdc1834d tmp/BC4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/BC4	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/tmp_BC1_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC1_visible.fastqsanger	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/tmp_BC1_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC1_visible_fastqsanger	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/tmp_BC2_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC2_visible.fastqsanger	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/tmp_BC2_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC2_visible_fastqsanger	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/tmp_BC3_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC3_visible.fastqsanger	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/tmp_BC3_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC3_visible_fastqsanger	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/tmp_BC4_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC4_visible.fastqsanger	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/tmp_BC4_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_BC4_visible_fastqsanger	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/tmp_unmatched_visible.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_unmatched_visible.fastqsanger	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/tmp_unmatched_visible_fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/tmp_unmatched_visible_fastqsanger	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp/unmatched
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp/unmatched	Fri Mar 11 17:24:31 2016 -0500
@@ -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 32304398ef67 -r e7b7cdc1834d tmp_stdio.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmp_stdio.txt	Fri Mar 11 17:24:31 2016 -0500
@@ -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