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Die with appropriate error message if we try to read past the end 

of a chromosome.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@261 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-04-02 16:44:32 +00:00
parent 24e8581c30
commit 3248176118
1 changed files with 7 additions and 2 deletions
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9
java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
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@ -123,11 +123,16 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
assert seekContigName.equals(currentContig.getName()) : String.format("only works on this contig, but the current %s and sought %s contigs are different!", currentContig.getName(), seekContigName);
// we're somewhere on this contig
if ( seekOffset < offset || seekOffset >= currentContig.length() ) {
// bad boy -- can't go backward safely or just beyond the contig length
if ( seekOffset < offset ) {
// bad boy -- can't go backward safely
throw new IllegalArgumentException(String.format("Invalid seek to %s from %s, which is usually due to out of order reads%n",
new GenomeLoc(currentContig.getName(), seekOffset), new GenomeLoc(currentContig.getName(), offset)));
}
else if ( seekOffset >= currentContig.length() ) {
// bad boy -- can't go beyond the contig length
throw new IllegalArgumentException(String.format("Invalid seek to %s, which is beyond the end of the contig%n",
new GenomeLoc(currentContig.getName(), seekOffset+1)));
}
else {
offset = seekOffset - 1;
return next();