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As the VCF guru, I'll take this one for Andrey. Someone has actually found a deletion at the beginning of the chromosome. Instead of failing with an ArrayIndexOutOfBoundsException, just don't try to print out the record. Our VCF writer doesn't really support this case (yet). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4199 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-09-03 03:27:43 +00:00
parent c45ffcdaed
commit fdaac4aa78
1 changed files with 6 additions and 0 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -731,6 +731,12 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
if ( event_length < 0 ) event_length = 0;
long start = call.getPosition()-1;
// If the beginning of the chromosome is deleted (possible, however unlikely), it's unclear how to proceed.
// The suggestion is instead of putting the base before the indel, to put the base after the indel.
// For now, just don't print out that site.
if ( start == 0 )
return;
long stop = start;
List<Allele> alleles = new ArrayList<Allele>(2);