# HG changeset patch
# User geert-vandeweyer
# Date 1406580044 14400
# Node ID e79b771cf3a9486fc65ac7a27c745825b32989fd
# Parent  f51dd12f22637ec80f49fb519d7b220f35f36448
Uploaded

diff -r f51dd12f2263 -r e79b771cf3a9 run_cf0611.pl
--- a/run_cf0611.pl	Mon Jul 28 13:34:56 2014 -0400
+++ b/run_cf0611.pl	Mon Jul 28 16:40:44 2014 -0400
@@ -189,7 +189,7 @@
 sub assemble {
     system("${SAMTOOLS}samtools view merged.sorted.final.temp.bam | sort -k 1,1 -k 2,2n -u | tee merged.sorted.final.unique.sam  | perl ${scriptspath}/split_for_velvet.pl pair1.fq pair2.fq single.fq");
     if(!(-s "pair1.fq")) {
-	print STDERR "No breakpoints supported by split reads.\n";
+	print STDOUT "No breakpoints supported by split reads.\n";
 	exit(1);
     }
 	system("${VELVET}velveth velvet_out 31 -fastq -shortPaired -separate pair1.fq pair2.fq -short single.fq > /dev/null 2>&1");