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corresponding fix for dealing with insertions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3739 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-08 05:25:03 +00:00
parent ada8c9931f
commit ed0d0d78fa
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
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@ -149,9 +149,9 @@ public class PickSequenomProbes extends RodWalker<String, String> {
String assay_sequence;
if ( vc.isSNP() )
assay_sequence = leading_bases + "[" + ref.getBaseAsChar() + "/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
assay_sequence = leading_bases + "[" + (char)ref.getBase() + "/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
else if ( vc.isInsertion() )
assay_sequence = leading_bases + "[-/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
assay_sequence = leading_bases + "[-/" + vc.getAlternateAllele(0).toString() + "]" + (char)ref.getBase() + trailing_bases;
else if ( vc.isDeletion() )
assay_sequence = leading_bases + "[" + new String(vc.getReference().getBases()) + "/-]" + trailing_bases.substring(vc.getReference().length()-1);
else