From 1284227acdd2c99295c49726d3c208f47fa138c7 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 8 Nov 2011 10:59:27 -0500
Subject: [PATCH] Squash SAMTools stderr chatter when using FreeBayes which
 would cause error state. FreeBayes should be updated to e.g. have access to
 built-in reference genomes, etc.

---
 tools/human_genome_variation/freebayes.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/human_genome_variation/freebayes.xml b/tools/human_genome_variation/freebayes.xml
index a5d579ee19f..50a906d0992 100644
--- a/tools/human_genome_variation/freebayes.xml
+++ b/tools/human_genome_variation/freebayes.xml
@@ -5,11 +5,11 @@
   </requirements>
   <description>Bayesian genetic variant detector</description>
   <command>
-    ln -s $reference localref.fa;
-    ln -s $bamfile localbam.bam;
-    samtools faidx localref.fa;
-    samtools sort localbam.bam localbam.bam;
-    samtools index localbam.bam;
+    ln -s $reference localref.fa &amp;&amp;
+    ln -s $bamfile localbam.bam &amp;&amp;
+    samtools faidx localref.fa 2&gt;&amp;1 || echo "Error running samtools faidx for FreeBayes" &gt;&amp;2 &amp;&amp;
+    samtools sort localbam.bam localbam.bam 2&gt;&amp;1 || echo "Error running samtools sort for FreeBayes" &gt;&amp;2 &amp;&amp;
+    samtools index localbam.bam 2&gt;&amp;1 || echo "Error running samtools index for FreeBayes" &gt;&amp;2 &amp;&amp;
     freebayes --fasta-reference localref.fa localbam.bam --vcf $output
             #if $params.source_select == "full":
                 $params.showRefRepeats