# HG changeset patch
# User stef
# Date 1412936179 14400
# Node ID 0220bfeefbc1e815f4f7dfdef84136cb72f199db
# Parent  2210b89487c6743c37be97d7fd41c3b618c18665
Uploaded

diff -r 2210b89487c6 -r 0220bfeefbc1 falco-call.sh
--- a/falco-call.sh	Fri Oct 10 06:13:06 2014 -0400
+++ b/falco-call.sh	Fri Oct 10 06:16:19 2014 -0400
@@ -62,10 +62,14 @@
 
 source $init_file
 
-echo "--- sam ---"
+echo "------ --- ------"
+echo "------ sam ------"
+echo "------ --- ------"
 samtools
-#echo "--- bcf ---"
-#bcftools
+echo "------ --- ------"
+echo "------ sam ------"
+echo "------ --- ------"
+bcftools
 #echo "--- snpsift ---"
 #java -jar $snpSift/SnpSift.jar
 #echo "--- snpeff ---"
@@ -73,13 +77,14 @@
 #echo "--- varscan ---"
 #java -jar $varScan
 
-exit 0
+## DEBUG
+#exit 0
 
 ## ----------
 ## create output files dir
 ## ----------
-mkdir $out_path
-mkdir $out_path/$bam_base
+#mkdir $out_path
+#mkdir $out_path/$bam_base
 
 ## ----------
 ## running analysis