# HG changeset patch
# User lparsons
# Date 1353445280 18000
# Node ID f0d19a935325073efc5e624c1c7068113bb7f3c7
# Parent  71eaf2e85ae721e14e69e249532d11f7e6e414af
Uploaded

diff -r 71eaf2e85ae7 -r f0d19a935325 README.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Tue Nov 20 16:01:20 2012 -0500
@@ -0,0 +1,19 @@
+== ea-utils Galaxy Wrapper ==
+
+This is a Galaxy wrapper for some ea-utils tools, fastq-join and sam-stats.
+
+** Installation **
+
+Installation from a tool shed provides the necessary tool dependencies.
+
+Otherwise, make sure fastq-join and sam-stats are in the path.
+Move the test data files to your galaxy root test-data.
+Move the xml files to a subdirectory of your tools directory and add lines in tool_conf.xml to point to them.
+Restart the Galaxy server.
+
+** Attribution **
+
+The ea-utils package and associated documentation can be found at: http://code.google.com/p/ea-utils/
+
+The galaxy wrapper code was written by Lance Parsons (lparsons@princeton.edu), Lewis-Sigler Institute for Integrative Genomics, Princeton University.
+The code is housed on BitBucket at: https://bitbucket.org/lance_parsons/ea_utils_galaxy_wrapper
diff -r 71eaf2e85ae7 -r f0d19a935325 sam-stats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam-stats.xml	Tue Nov 20 16:01:20 2012 -0500
@@ -0,0 +1,83 @@
+<tool id="sam_stats" name="sam-stats" version="0.1">
+    <description> - Compute statistics from SAM or BAM files</description>
+    <requirements>
+        <requirement type="package" version="1.1.2-484">ea-utils</requirement>
+    </requirements>
+    <command>
+        sam-stats
+        $trackMultAlign
+        $reportAllChr
+        #if $rnaSeqStats:
+        -R $rnaSeqStatsFile
+        #end if
+        #if $input.extension == "bam":
+        -B
+        #end if
+        -S $histBinSize
+        $input
+        &gt; $samStats
+    </command>
+    <inputs>
+        <param format="sam, bam" name="input" type="data" label="SAM/BAM File" />
+        <param name="trackMultAlign" type="boolean" value="False" truevalue="-D" falsevalue="" label="Keep track of multiple alignments (slower!)" />
+        <param name="reportAllChr" type="boolean" value="False" truevalue="-A" falsevalue="" label="Report all chr sigs, even if there are more than 1000" />
+        <!-- <param name="numReadsSubsample" type="integer" value="1000000" min="1" max="1000000" label="Number of reads to sample for per-base statistics (max 1,000,000)" /> -->
+        <param name="histBinSize" type="integer" value="30" min="1" label="Number of bins per chromosome for reads by chromosome &quot;histogram&quot;" />
+        <param name="rnaSeqStats" type="boolean" value="False" label="Output RNA-Seq statistics (coverage, 3 prime bias, etc.)" />
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="samStats" label="${tool.name} on ${on_string}"/>
+        <data format="tabular" name="rnaSeqStatsFile" label="${tool.name} on ${on_string} (RNA-Seq Stats)"> <filter>rnaSeqStats</filter>
+        </data>
+    </outputs>
+
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Unknown error occurred" />
+    </stdio>
+
+    <tests>
+        <test>
+            <param name="input" value="test.sam" />
+            <output name="samStats" file="testout.txt" />
+        </test>
+    </tests>
+
+    <help>
+Overview
+--------
+sam-stats computes varius statics on SAM/BAM alignment files.
+
+Complete Stats::
+
+  &lt;STATS&gt;           : mean, max, stdev, median, Q1 (25 percentile), Q3
+  reads             : # of entries in the sam file, might not be # reads
+  phred             : phred scale used
+  bsize             : # reads used for qual stats
+  mapped reads      : number of aligned reads (unique probe id sequences)
+  mapped bases      : total of the lengths of the aligned reads
+  forward           : number of forward-aligned reads
+  reverse           : number of reverse-aligned reads
+  snp rate          : mismatched bases / total bases
+  ins rate          : insert bases / total bases
+  del rate          : deleted bases / total bases
+  pct mismatch      : percent of reads that have mismatches
+  len &lt;STATS&gt;       : read length stats, ignored if fixed-length
+  mapq &lt;STATS&gt;      : stats for mapping qualities
+  insert &lt;STATS&gt;    : stats for insert sizes
+  &lt;CHR&gt;           : percentage of mapped bases per chr, followed by a signature
+
+Subsampled stats (1M reads max)::
+
+  base qual &lt;STATS&gt; : stats for base qualities
+  A,T,C,G       : base percentages
+
+Meaning of the per-chromosome signature:
+
+  A ascii-histogram of mapped reads by chromosome position.  It is only output if the original SAM/BAM has a header. The values are the log2 of the # of mapped reads at each position + ascii '0'.
+
+See http://code.google.com/p/ea-utils/wiki/SamStatsDetails for more information on each stat, how it's calculated and what it means.
+
+This tool uses the sam-stats program that is part of the ea-utils suite. See http://code.google.com/p/ea-utils/wiki/SamStats for details.
+    </help>
+</tool>
diff -r 71eaf2e85ae7 -r f0d19a935325 test-data/test.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.sam	Tue Nov 20 16:01:20 2012 -0500
@@ -0,0 +1,100 @@
+GEN-SEQ-ANA_0001:1:1:17434:14109#0/1	0	PCRPRIMER1	5	255	33M	*	0	0	ATACGGCGACCACCGAGATCTACACTCTTTCCC	?<??>>BB>>A5AAA;;9:B<A?:AAA<B<AAA	XA:i:0	MD:Z:33	NM:i:0
+GEN-SEQ-ANA_0001:1:1:4183:5576#0/1	0	PCRPRIMER1+1	1	255	38M	*	0	0	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCT	AA=A=7=>;<BB8;>5>>?:B>BAABBBBBBBBABBB;	XA:i:0	MD:Z:38	NM:i:0
+GEN-SEQ-ANA_0001:1:1:16837:9043#0/1	0	PCRPRIMER1+1	14	255	27M	*	0	0	CCACCGAGATCTACACTCTTTCCCTAC	?BB?ABB?BBB<7A5?7??A?<AA?A?	XA:i:0	MD:Z:27	NM:i:0
+GEN-SEQ-ANA_0001:1:1:6753:19078#0/1	0	PCRPRIMER1+1	58	255	25M	*	0	0	TAATGATACGGCGACCACCGAGATC	A:BABA:AA<?B<<?BBBBBB@BBB	XA:i:0	MD:Z:25	NM:i:0
+GEN-SEQ-ANA_0001:1:1:14641:6640#0/1	0	PCRPRIMER1+1	58	255	43M	*	0	0	TAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACAC	AC@CB>:CC>CCCCCC?@CCBB<?@B@BAB@ABBBBBB5:?5?	XA:i:0	MD:Z:43	NM:i:0
+GEN-SEQ-ANA_0001:1:1:18498:19719#0/1	0	PCRPRIMER1+1	58	255	38M	*	0	0	TAATGATACGGCGACCACCGAGATCTACACTCTTTCCC	CCCCCCCCCBCCACCC@CCC@BCCCCCC@CCCCCCCCC	XA:i:0	MD:Z:38	NM:i:0
+GEN-SEQ-ANA_0001:1:1:5165:8271#0/1	0	PCRPRIMER1+2	1	255	37M	*	0	0	AATGATACGGCGACCACCGAGATCTACACTCTTTCCC	CC=CC>CC:@CCC@C>BAB<B>AAA88?>>ABBB:AA	XA:i:0	MD:Z:37	NM:i:0
+GEN-SEQ-ANA_0001:1:1:3890:20139#0/1	0	PCRPRIMER2+1	34	255	23M	*	0	0	TAATGATACGGCGACCACCGAGA	CCCCCC<CBB;;C@CC5<CABB7	XA:i:0	MD:Z:23	NM:i:0
+GEN-SEQ-ANA_0001:1:1:6236:11228#0/1	0	PCRPRIMER2+1	34	255	20M	*	0	0	TAATGATACGGCGACCACCG	CCCCCC8CCCCC=CC?AAAA	XA:i:0	MD:Z:20	NM:i:0
+GEN-SEQ-ANA_0001:1:1:13390:7511#0/1	0	PCRPRIMER2+1	34	255	48M	*	0	0	TAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGC	CCACBCBBBCCCCCCC?CCC;C?CCC?CCCCCCCCCCCACCCC;=>8A	XA:i:0	MD:Z:48	NM:i:0
+GEN-SEQ-ANA_0001:1:1:16810:9063#0/1	0	PCRPRIMER2+1	34	255	45M	*	0	0	TAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA	CCCCCCCCBCCCBBCCCCCCCCCCCCCCBA=@CCCCBC5B@9@@@	XA:i:0	MD:Z:45	NM:i:0
+GEN-SEQ-ANA_0001:1:1:1127:14386#0/1	4	*	0	0	*	*	0	0	TGAATTCATGAATGGAAAAA	?ACC<@>69@6>@BB?@:==	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1210:17845#0/1	4	*	0	0	*	*	0	0	GAGATAATTCAAAATCTTGCCGAT	>===>>@@@=<89A<B:@:BAA@@	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1260:17853#0/1	4	*	0	0	*	*	0	0	GTACAAATTCAGGACCACGCGTAAACGTCACC	CCCCCB;ACBBB6@BB@BBB=A?A>6>AB?>B	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1227:4069#0/1	4	*	0	0	*	*	0	0	TCGAGAATTCTTTATCAACCTCGTT	=CCCCCBC6@BCCC=9BA7A>>BB>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1309:16895#0/1	4	*	0	0	*	*	0	0	GTACAAATTCCCTCATTCTTGGATTTGTA	CA>CC@BBC8C@C>=C5<CCC@?CC;?>;	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1290:1939#0/1	4	*	0	0	*	*	0	0	TACGTAATTCCGTGTCGGAGCCCGT	??B:6>B;>AB=>B>B:BB>?A<6?	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1311:12611#0/1	4	*	0	0	*	*	0	0	AAATTCGTTTATTTTTGTATTT	BBBBB@@@@@@@B:====:BBA	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1312:13847#0/1	4	*	0	0	*	*	0	0	CGATAAATTCCTTGCTTCAACGATGCA	?BB>=8CC@??CCCC@B?>CC:CCC:8	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1327:14127#0/1	4	*	0	0	*	*	0	0	ATAAATTCAGAATAGTTTCACT	=A:??B>=;B@A;97C>B@=6B	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1328:16612#0/1	4	*	0	0	*	*	0	0	GAGATAATTCTTCTCATCGG	@@@8@;C@C@CC=BC=>=AA	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1339:13574#0/1	4	*	0	0	*	*	0	0	TTCTGTGATAATTTCAATATTGCC	CB8B>=B=ABBBB:=BABBB@>=6	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1343:12008#0/1	4	*	0	0	*	*	0	0	TTCGGCACTTTTCAGCACAATTTTCA	CA=ACC@CC@BB=?AC??CC?CC?<C	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1353:17775#0/1	4	*	0	0	*	*	0	0	CGATAACTTCCCAACAGTGTTGTAAAG	>5CBC?8?C=?ACBC>CCBB@=CAA8:	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1358:3384#0/1	4	*	0	0	*	*	0	0	AACAAACCATGTTTTGCCCTCAAACAG	B8:BBBBB:BBB=BBBA@<BBB>BB:9	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1361:15054#0/1	4	*	0	0	*	*	0	0	ATGCTAATTCAGTAGCTATTGTTCTCCAAAT	BCC:?CA?C?=CC?ABC@<?B@C@CC@8C>C	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1362:13972#0/1	4	*	0	0	*	*	0	0	GTAATTCTTCGCGAGTCTTTG	@>C?CA?:@??@@@@CC?C?B	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1363:2154#0/1	4	*	0	0	*	*	0	0	AGCTGAATTCTAGAAATGAAGAATATTTTTATTTATTTTCAG	CB@C?B;CC=CAAC@@>:C?@:???CCBB>8>>>>?C>6>A?	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1373:2799#0/1	4	*	0	0	*	*	0	0	GAGATAATTCAAAACTACTACTGTAGAGGGGTACTG	?BABACCCC@B=<=@@?8B><@B@>BAAB9<@<>@B	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1374:3530#0/1	4	*	0	0	*	*	0	0	GAGATAATTCTTCCTCCTTAA	AAAC8A=CA>CC@CC:B7ACC	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1379:7364#0/1	4	*	0	0	*	*	0	0	CGCCAACCAAACCGATTGGCC	=???A;CCC?CCABCB8>CCC	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1382:18005#0/1	4	*	0	0	*	*	0	0	GTAGCGAGTGACTCCAGTATGGAT	?CBB>=BBB:@B;>><<><@>@?7	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1385:14548#0/1	4	*	0	0	*	*	0	0	TTCCTATTCAACTCCTCAATT	8=9=AA:A@=?AA@@@:@?AA	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1387:6982#0/1	4	*	0	0	*	*	0	0	ATTCGCGCCGATTGGGATTTTTG	6B?>:A=:A?7:<A<BBB?;?6<	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1390:2086#0/1	4	*	0	0	*	*	0	0	AATAAAACTTAAAATCTCAG	BBA?B:::A6B>A>B=B=BB	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1392:4030#0/1	4	*	0	0	*	*	0	0	AGCTGAATTCGAGCCCATTGATGA	?@6C@C@<A??CCC=C?C?C:A?A	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1397:15413#0/1	4	*	0	0	*	*	0	0	TCTTCGAAAAAACAAGCATCTACGTCTTG	7?BA?<B?B@<:::;;<>>BB<<<;95BA	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1403:14145#0/1	4	*	0	0	*	*	0	0	ATGCTAATTCTCGTGGAACTCG	CA>C=CC@CA?8???7C7@=??	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1404:13576#0/1	4	*	0	0	*	*	0	0	CGATAAATTCTCTGAAAATGCATA	>BB=:BBBB@B@=B@BB=BBAB;B	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1408:13430#0/1	4	*	0	0	*	*	0	0	GAACAATAAAACCTCCTGTC	@8B5@AA?@A==AAA=AA6@	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1410:6288#0/1	4	*	0	0	*	*	0	0	TCCGAAAACCAAATTTTACTG	9?>B5:CBC:@C@CCB?CCCB	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1420:17657#0/1	4	*	0	0	*	*	0	0	TTCAATGAGAGAATCCGCGACGAAAATGG	CC?CCC?BB?C:CAAB5AB>BB>BA8<B8	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1421:18483#0/1	4	*	0	0	*	*	0	0	GTACAAATTCAGAAAATATTTTATT	BC?CC@CBCA@BC@AA:6B@=BAB8	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1422:15203#0/1	4	*	0	0	*	*	0	0	GTACAAATTCGTGTCGAAATTGAAAAAAAAAG	CCC?CCCBCACC@@@CCCACC@=C;8?;98>>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1423:18328#0/1	4	*	0	0	*	*	0	0	ATAAATTCATCGACAGGTACCTTCTAT	<@@<>?B>>AB=>BBB>B=BBBA7>>6	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1426:4162#0/1	4	*	0	0	*	*	0	0	GCTAATTCCTATGGTTATAACTCTAAAACGGGTC	7==8<>@9B@?=5ACACA>>BCC?>C=?B>9@8;	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1426:18217#0/1	4	*	0	0	*	*	0	0	TCCTTCAAAAATCATCACTGAAA	>7:>@>@AA=@A:A@6@7A;>55	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1428:17122#0/1	4	*	0	0	*	*	0	0	GTACAAATTCATCTAATGGTCTAACTTTATA	C?CC8CCCBA@@=C>AAABC8BC:CCBACCC	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1434:13892#0/1	4	*	0	0	*	*	0	0	GTACAAATTCGCCAAGCGTTGGATTG	A???88@:;=>=?@@>BBB6A>AA5>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1441:16403#0/1	4	*	0	0	*	*	0	0	TGAATTCTGGCACTTCGGCGATT	B>B@?B<BB?A@>BB@@>BAAB:	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1445:8376#0/1	4	*	0	0	*	*	0	0	TGAATATGAAATTCGTAAATAGCGTGTT	@@CCC@>CBCC?CCC<CCBB?B?C@?@<	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1449:14365#0/1	4	*	0	0	*	*	0	0	TTCTCCAGGTACATCTGTCTGAAA	CC<CCBCCB@@BB>@BBBBBBBB>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1451:7415#0/1	4	*	0	0	*	*	0	0	CTCTTAATTCAAGTCCATATTCTCCTTGTAACCCCAAGTGATACAATATTTGATT	BBA@;CCAC>@@CC>CBCC?BCCBBC<B=CBC=?7=<BABCC;@<68AA;==:=?	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1452:4973#0/1	4	*	0	0	*	*	0	0	AGCTGAATTCTTGCTAAGCCGTGAATACAC	CA<C;>AAAABCCCBCCCBC@CACAC;CC<	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1455:18050#0/1	4	*	0	0	*	*	0	0	AGCTGAATTCCAGACATTATAGAAAA	BCCCC@=B@>>?C>CCCC?:CC:C=>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1455:12928#0/1	4	*	0	0	*	*	0	0	TCGAGAATTCCACATCACTTCTAT	@?@@;CCCC@B:C:CBBB=6<B8>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1456:13493#0/1	4	*	0	0	*	*	0	0	TTCATATTGGGTTTCTACCGCGAC	AB>B=?AA>B@BB>=BAAB=BBB>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1456:4776#0/1	4	*	0	0	*	*	0	0	ATGCTAATTCACATTCATGATT	CCCA=A@C@<CCCCCCC?A@C=	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1464:19773#0/1	4	*	0	0	*	*	0	0	TAAATTCTACTTCAAGGCGTGAT	=@B>@@<BBBBB@BBBB@B=<<?	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1469:15650#0/1	4	*	0	0	*	*	0	0	TACGTAATTCACTGCACTAATC	B=>C@C5C???BCCBCCC@?CC	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1469:15421#0/1	4	*	0	0	*	*	0	0	CGATAAATTCTGCCGGCAGAACTACGCATTT	AC;>CACCB8?CCA;ACBCBBC?CCAC=CCC	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1472:17572#0/1	4	*	0	0	*	*	0	0	TTCTACCCGGAACTCTTAAACAGAAGCGAGGC	CC>B@@:BB>>>B>B<BBB:B@B7@@=A<BBB	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1473:13951#0/1	4	*	0	0	*	*	0	0	AAATTTTTAAAAAAAATGTTTG	BCCCCCCC>C=CBC@8>CCC=C	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1473:13352#0/1	4	*	0	0	*	*	0	0	TCTGTGGAATTAACAATCACAATAACTAAAG	C?@BC@B<C=CC;C=CCCBCB8CA7C?CCC?	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1475:14575#0/1	4	*	0	0	*	*	0	0	TACGTAATTCGAAATTTGAG	?CB@C==AA?C=CCCBB:@B	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1480:6616#0/1	4	*	0	0	*	*	0	0	GTACAAATTCGAGCGCAAAGG	C;CCCCCCC?C@C9CC?CCC:	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1481:5435#0/1	4	*	0	0	*	*	0	0	GTACAAATTATGAATAGAGAACTTTTA	B@B6BBB=B>@@=@=@@BBBB>B?>B=	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1481:5276#0/1	4	*	0	0	*	*	0	0	GTACAAATTCGAATGAAATCATA	CCCCBBCDB@C=CDACCC=C?C>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1482:10064#0/1	4	*	0	0	*	*	0	0	CGATAAATTCAATTTGAAAA	CC=CCC6C@;CCCBCAB?9B	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1484:2325#0/1	4	*	0	0	*	*	0	0	AATTCCAACCACCATTGGAA	@A@=>@C??@C7CB@B6?:?	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1487:6701#0/1	4	*	0	0	*	*	0	0	CTCATTCATCTAGATATTTCTGATTTATCGTTGTTC	@9<?C@?BCCBCB@6@@AAA<<<<AB:BB@?@B6>>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1487:3645#0/1	4	*	0	0	*	*	0	0	CTAATTCGTGTAATAATTGTGTT	>87?@@>><9C:@7<A<BB?;>B	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1488:9645#0/1	4	*	0	0	*	*	0	0	ATGCTAATTCGAAGTGCGTATCTCTCGGT	ACCCCC8C@>>BBB=BB=A>BBBBB6B?>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1489:3252#0/1	4	*	0	0	*	*	0	0	TAAATTCTGAAAAATGTATTT	@<@@B@@=?C:C>>>B@A6A8	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1492:14525#0/1	4	*	0	0	*	*	0	0	AACTTCGAATATTAACAACA	@7:@>@@5C@>@@@C@@?B@	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1493:11409#0/1	4	*	0	0	*	*	0	0	CGAAACGGGCGTTGAGGCGTTTT	<BAB?>>=B6BBBBAB@=BB>BB	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1494:17779#0/1	4	*	0	0	*	*	0	0	TTTTCCTGAAAAATGTTCAACCTGATTATT	:;A;:?:A>A8A:A=?AAA@@:=55AA6@@	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1495:12537#0/1	4	*	0	0	*	*	0	0	GTACAAATTCACAATAATTA	BCCCBCCBCA;CCCBB@>>8	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1495:14319#0/1	4	*	0	0	*	*	0	0	ATTCGCCAAATTTGGCGTTAG	<?A>CCCCACBBCB@CCCACA	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1496:18187#0/1	4	*	0	0	*	*	0	0	AGGCGCGGCCAGCGGCTGGG	<:B<<6B6<>A?BBB:5A6A	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1496:10780#0/1	4	*	0	0	*	*	0	0	GAAATTCCCAAGAAACCCAAG	C:?7@??CACCBCCC=8AA:6	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1497:8211#0/1	4	*	0	0	*	*	0	0	CGATAAATTCCAAAGTTTGTGAATTT	BCCCCC?C@?<::A:?AA?AB?:B@<	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1498:13789#0/1	4	*	0	0	*	*	0	0	ATGCTAATTCTTTCGGAAACGAGACCATCTGA	>C8C>CC>B@==C@AC?C8@B?:6<AA?A?AB	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1501:3386#0/1	4	*	0	0	*	*	0	0	GTACAAATTCAGTAGTTTTG	?<=8?76@>;<C>AA@BBA@	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1502:11211#0/1	4	*	0	0	*	*	0	0	ATTCGTACTCGTGATTTTCGAACAATCCAGT	@AB=CCCCCCCBBA;CACCCB@A@C==C@CA	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1506:3772#0/1	4	*	0	0	*	*	0	0	CCATAAAATTATTGTCAATTTTCAAT	??:@?:BC:C?CC>C<?=@>BCCC::	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1506:13304#0/1	4	*	0	0	*	*	0	0	AATTCGACATCGCAAGTGAG	AAA?>?CC>CBB?CBCBCA>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1506:17897#0/1	4	*	0	0	*	*	0	0	TGAATTCCGCCTTGGAGACAATGTTCT	B:6<BB8B?=B>>?:B=B=BB>=?BBA	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1507:13225#0/1	4	*	0	0	*	*	0	0	TGCTAATTCTAATTTTCATGTATACTAAACCCCCAC	@?C>B8@<9B?C=CB5B66A<<?6?A>AA8?A<<A6	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1508:6179#0/1	4	*	0	0	*	*	0	0	GTCAAAAGTAGAGAAAAAAAA	><B=9<@B?@@BAB@A@9=9=	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1508:8256#0/1	4	*	0	0	*	*	0	0	ATTCTCGCCAGCCTTTTTAAGTCGAGTTT	ABB<ABA>BAAA=?B???6BB=<BAB=B?	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1508:11605#0/1	4	*	0	0	*	*	0	0	TACGCAATTCTTCTCAAAAATTC	B==B9=:=B=CBCCCB:B5B5>>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1510:9250#0/1	4	*	0	0	*	*	0	0	AAAAACTGAAAAATTAAGATTAAAAGC	A=?A6AA@?AAA@@AA:A8A@:>8AA5	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1510:4740#0/1	4	*	0	0	*	*	0	0	CTCTTAATTCATTTTTTTTTCAGTTTTAAAGGTG	BC;BBCCCC@>CC;CCB>8>=BBB6BBBB=B?=B	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1511:8709#0/1	4	*	0	0	*	*	0	0	TTCACTTTCTATGGTTATTTT	CC@=ACCCCCB?CCBBCCC=>	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1513:14094#0/1	4	*	0	0	*	*	0	0	AGCTGAATTCCAATTCTCTATCACGATT	BC8CCBCC@;CCC8CCCCCACCCAB@@@	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1515:16388#0/1	4	*	0	0	*	*	0	0	AGCTGAATTCGCCAAGCGTTGGAT	BC;CCC@C?;=CCCCCCC@C;C@C	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1516:14913#0/1	4	*	0	0	*	*	0	0	CTAATTCGTCCAGATTTCCA	C:BCCB?CCBBACCBBCCCC	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1517:17176#0/1	4	*	0	0	*	*	0	0	CGATAAATTCTAATTTTGCCA	>C<@CBA9B?BB?CBCABCCB	XM:i:0
+GEN-SEQ-ANA_0001:1:1:1520:6860#0/1	4	*	0	0	*	*	0	0	GTACAAATTCTTGAGAGACAGAATT	C??C;CCCC?CCCCCCC@BC@C?AC	XM:i:0
diff -r 71eaf2e85ae7 -r f0d19a935325 test-data/testout.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testout.txt	Tue Nov 20 16:01:20 2012 -0500
@@ -0,0 +1,29 @@
+reads	100
+version	1.32
+mapped reads	11
+mapped bases	377
+phred	33
+forward	0
+reverse	11
+len max	48
+len mean	34.2727
+len stdev	9.4137
+mapq mean	255.0000
+mapq stdev	0.0000
+mapq Q1	255.00
+mapq median	255.00
+mapq Q3	255.00
+snp rate	0.000000
+pct mismatch	0.0000
+base qual mean	31.5650
+base qual stdev	3.2627
+%A	27.5862
+%C	34.4828
+%G	16.7109
+%T	21.2202
+%PCRPRIMER1	8.753316
+%PCRPRIMER1+1	45.358090
+%PCRPRIMER1+2	9.814324
+%PCRPRIMER2+1	36.074271
+num ref seqs	4
+num ref aligned	4