From a4f910c7302a5257d934ab502aee609a89701126 Mon Sep 17 00:00:00 2001
From: Kelly Vincent <kpvincent@bx.psu.edu>
Date: Tue, 8 Mar 2011 16:17:09 -0500
Subject: [PATCH] Update SRMA test files so that functional tests pass

---
 tools/sr_mapping/srma_wrapper.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/sr_mapping/srma_wrapper.xml b/tools/sr_mapping/srma_wrapper.xml
index 75c3f0c36b4..a3009d0bf11 100644
--- a/tools/sr_mapping/srma_wrapper.xml
+++ b/tools/sr_mapping/srma_wrapper.xml
@@ -82,7 +82,7 @@
           Prepare bam index file:
           samtools index srma_in1.bam
           Run SRMA:
-          java -jar "srma.jar" I=srma_in1.bam O=srma_out1.bam R=/afs/bx.psu.edu/depot/data/genome/hg18/srma_index/chr21.fa
+          java -jar srma.jar I=srma_in1.bam O=srma_out1.bam R=/afs/bx.psu.edu/depot/data/genome/hg18/srma_index/chr21.fa
           To create the bam file first, start with a sam file (srma_in1.sam) generated with a run using the chr21 fasta file and which contains the header. Run before samtools index:
           samtools view -bt /afs/bx.psu.edu/depot/data/genome/hg18/sam_index/chr21.fa -o srma_in1.u.bam srma_in1.sam
           samtools sort srma_in1.u.bam srma_in1
@@ -97,13 +97,13 @@
           <!-- Commands to run to prepare test files (uses custom genome):
           Prepare custom dict/index files:
           samtools faidx srma_in2.fa
-          java -cp "srma.jar" net.sf.picard.sam.CreateSequenceDictionary R=srma_in2.fa O=srma_in2.dict
+          java -cp srma.jar net.sf.picard.sam.CreateSequenceDictionary R=srma_in2.fa O=srma_in2.dict
           Prepare bam index file:
           samtools index srma_in3.bam
           Run SRMA:
           java -jar "srma.jar" I=srma_in3.bam O=srma_out2.bam R=srma_in2.fa OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=2 RANGES=null RANGE=null CORRECT_BASES=true USE_SEQUENCE_QUALITIES=true MAX_HEAP_SIZE=8192
-          To create the bam file first, the sam file needs to have been run with the same reference file (srma_in2.fa) and have the header present. Run these commands before samtools index:
-          samtools view -bt srma_in2.fa -o srma_in3.u.bam srma_in1.sam
+          To create the bam file first, the sam file needs to have been run with the same reference file (srma_in2.fa) and have the header present. For instance:
+          samtools view -bT srma_in2.fa -o srma_in3.u.bam srma_in3.sam
           samtools sort srma_in3.u.bam srma_in3
           -->
           <param name="refGenomeSource_type" value="history" />