From 872f32a3938c2a7ee1b0f3138e6a569b3041eac9 Mon Sep 17 00:00:00 2001 From: Daniel Cameron Date: Mon, 10 Jun 2019 15:41:16 +1000 Subject: [PATCH] Fixed IntervalBed error message --- example/gridss.sh | 2 +- example/gridss_lite.sh | 3 ++- src/main/java/au/edu/wehi/idsv/bed/IntervalBed.java | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/example/gridss.sh b/example/gridss.sh index 1a660ecb7..e05428fd8 100644 --- a/example/gridss.sh +++ b/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 diff --git a/example/gridss_lite.sh b/example/gridss_lite.sh index 431d2795a..e10ba95f7 100644 --- a/example/gridss_lite.sh +++ b/example/gridss_lite.sh @@ -109,13 +109,13 @@ 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 @@ -123,6 +123,7 @@ if [[ "$assembly" == "" ]] ; then echo "Specify assembly bam location using the --assembly command line argument" 1>&2 fi assembly=$(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 diff --git a/src/main/java/au/edu/wehi/idsv/bed/IntervalBed.java b/src/main/java/au/edu/wehi/idsv/bed/IntervalBed.java index 7abdef7a4..fbd097b7a 100644 --- a/src/main/java/au/edu/wehi/idsv/bed/IntervalBed.java +++ b/src/main/java/au/edu/wehi/idsv/bed/IntervalBed.java @@ -66,7 +66,7 @@ private static RangeSet 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); }