zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
This commit is contained in:
ebanks 2010-04-09 05:52:53 +00:00
parent fba48b515a
commit 3f2455e346
1 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
View File

@ -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);
}