Fixed IntervalBed error message

example/gridss.sh

@@ -89,13 +89,13 @@ if [[ "$workingdir" == "" ]] ; then
 	echo "Working directory must be specified. Specify using the --workingdir command line argument" 1>&2
 	exit 2
 else
-	workingdir=$(readlink -f $workingdir)
 	if [[ ! -d $workingdir ]] ; then
 		if ! mkdir -p $workingdir ; then
 			echo Unable to create working directory $workingdir 1>&2
 			exit 2
 		fi
 	fi
+	workingdir=$(readlink -f $workingdir)
 	echo "Using working directory $workingdir" 1>&2
 fi
 if [[ "$assembly" == "" ]] ; then

example/gridss_lite.sh

@@ -109,20 +109,21 @@ if [[ "$workingdir" == "" ]] ; then
 	echo "Working directory must be specified. Specify using the --workingdir command line argument" 1>&2
 	exit 2
 else
-	workingdir=$(readlink -f $workingdir)
 	if [[ ! -d $workingdir ]] ; then
 		if ! mkdir -p $workingdir ; then
 			echo Unable to create working directory $workingdir 1>&2
 			exit 2
 		fi
 	fi
+	workingdir=$(readlink -f $workingdir)
 	echo "Using working directory $workingdir" 1>&2
 fi
 if [[ "$assembly" == "" ]] ; then
 	echo $USAGE_MESSAGE  1>&2
 	echo "Specify assembly bam location using the --assembly command line argument" 1>&2
 fi
 assembly=$(readlink -f $assembly)
+echo Using assembly output $assembly
 if [[ "$reference" == "" ]] ; then
 	echo $USAGE_MESSAGE  1>&2
 	echo "Specify reference location using the --reference command line argument" 1>&2

src/main/java/au/edu/wehi/idsv/bed/IntervalBed.java

@@ -66,7 +66,7 @@ private static RangeSet<Long> toRangeSet(LinearGenomicCoordinate linear, File be
 				int end = feat.getEnd();
 				int referenceIndex = linear.getDictionary().getSequenceIndex(chr);
 				if (referenceIndex < 0) {
-					String msg = String.format("Error loading record %d of %s: '%s' not found in reference genome.");
+					String msg = String.format("Error loading record %d of %s: '%s' not found in reference genome.", lineno, bed, chr);
 					log.error(msg);
 					throw new IllegalArgumentException(msg);
 				}