From 3f2455e34697ab60cba0f3062ffe7e08eea3f9c8 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 9 Apr 2010 05:52:53 +0000 Subject: [PATCH] Better error message as suggested by James P git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3141 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/utils/GenomeLocParser.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index d98a94030..c9e600ece 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -198,7 +198,7 @@ public class GenomeLocParser { // is the contig valid? if (!isContigValid(contig)) - throw new StingException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference."); + throw new StingException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?"); if (stop == Integer.MAX_VALUE && hasKnownContigOrdering()) // lookup the actually stop position! @@ -276,7 +276,7 @@ public class GenomeLocParser { */ public static GenomeLoc parseGenomeLoc(final String contig, long start, long stop) { if (!isContigValid(contig)) - throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference."); + throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?"); return new GenomeLoc(contig, getContigIndex(contig,true), start, stop); }