From ce2866122d99faa9d2dfe99fb9d5ec8c6173506d Mon Sep 17 00:00:00 2001
From: corin <corin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 3 Feb 2011 18:34:07 +0000
Subject: [PATCH] Calls the bams pulled down from firehose cleaned by default

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5188 348d0f76-0448-11de-a6fe-93d51630548a
---
 shell/getFirehosePipelineYaml.sh | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/shell/getFirehosePipelineYaml.sh b/shell/getFirehosePipelineYaml.sh
index fde8b52fb..a6e1ef10c 100755
--- a/shell/getFirehosePipelineYaml.sh
+++ b/shell/getFirehosePipelineYaml.sh
@@ -114,3 +114,13 @@ END {
         printf "\n  ]"
     print "\n}"
 }' > $PIPELINE_YAML_FILE
+
+hg19=`grep "assembly19" -c $PIPELINE_YAML_FILE`
+
+if [ "$hg19" -ne 0 ]; then
+    sed 's/\/humgen.*rod/\/humgen\/gsa-hpprojects\/GATK\/data\/dbsnp_132_b37.vcf/' $PIPELINE_YAML_FILE > yaml2 
+    mv yaml2 $PIPELINE_YAML_FILE
+fi
+
+sed 's/recalibrat/clean/' $PIPELINE_YAML_FILE > yaml2
+mv yaml2 $PIPELINE_YAML_FILE