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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
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ebanks 2010-04-09 05:52:53 +00:00
parent fba48b515a
commit 3f2455e346
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
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@ -198,7 +198,7 @@ public class GenomeLocParser {
// is the contig valid? // is the contig valid?
if (!isContigValid(contig)) 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()) if (stop == Integer.MAX_VALUE && hasKnownContigOrdering())
// lookup the actually stop position! // lookup the actually stop position!
@ -276,7 +276,7 @@ public class GenomeLocParser {
*/ */
public static GenomeLoc parseGenomeLoc(final String contig, long start, long stop) { public static GenomeLoc parseGenomeLoc(final String contig, long start, long stop) {
if (!isContigValid(contig)) 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); return new GenomeLoc(contig, getContigIndex(contig,true), start, stop);
} }