# HG changeset patch
# User stef
# Date 1420026828 18000
# Node ID b4e2b4efae619bafd3b06a405a07c7bde2c68e8e
# Parent  493bbb54ca1a39baf4ae8badc060b27f8e44e4c1
Uploaded

diff -r 493bbb54ca1a -r b4e2b4efae61 falco-call.sh
--- a/falco-call.sh	Wed Dec 31 06:30:53 2014 -0500
+++ b/falco-call.sh	Wed Dec 31 06:53:48 2014 -0500
@@ -11,7 +11,16 @@
 bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
 
 ## ----------
-## Create extra init script
+## make sure all is ok
+## ----------
+if [ ! -f $REF_FILE".fai" ]
+then
+	echo "No FAI index (fai) found for reference fasta [$REF_FILE]"
+	exit "No FAI index (fai) found for reference fasta [$REF_FILE]"
+fi
+
+## ----------
+## set params
 ## ----------
 if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default somehow is "None"
 then 
@@ -34,15 +43,15 @@
 if [ $DEBUG ]
 then
 	DBS="[INFO] "
-	echo $DBS"FILTER:  "$filter_file
-	echo $DBS"MANIFES: "$manifest_file
-	echo $DBS"REFFILE: "$REF_FILE
-	echo $DBS"DB_KEY:  "$DB_KEY
-	echo $DBS"REF_SRC: "$REF_SOURCE
-	echo $DBS"BAMFILE: "$bam_file
-	echo $DBS"BAMNAME: "$bam_name
-	echo $DBS"BAMBASE: "$bam_base
-	echo $DBS"OUTPATH: "$out_path
+	echo $DBS"FILTER:   "$filter_file
+	echo $DBS"MANIFEST: "$manifest_file
+	echo $DBS"REF FILE: "$REF_FILE
+	echo $DBS"DB KEY:   "$DB_KEY
+	echo $DBS"REF SRC:  "$REF_SOURCE
+	echo $DBS"BAM FILE: "$bam_file
+	echo $DBS"BAM NAME: "$bam_name
+	echo $DBS"BAM BASE: "$bam_base
+	echo $DBS"OUT PATH: "$out_path
 fi
 
 ## ----------