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Ugly one-off error fixed in building design sequences for indels: the event position is immediately *before* the event, so the ref base at the current locus is the base immediately *before* [ref/alt] element 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5103 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-01-28 02:53:03 +00:00
parent 3e9f185dad
commit ac3fd567b4
1 changed files with 7 additions and 2 deletions
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9
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
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@ -120,6 +120,11 @@ public class PickSequenomProbes extends RodWalker<String, String> {
logger.debug(" "+VCs.size()+ " variants at the locus");
}
// System.out.print("At locus "+ref.getLocus()+": ");
// for ( VariantContext vc : VCs ) {
// System.out.println(vc.toString());
// }
// little optimization: since we may have few events at the current site on the reference,
// we are going to make sure we compute the mask and ref bases only once for each location and only if we need to
boolean haveMaskForWindow = false;
@ -199,9 +204,9 @@ public class PickSequenomProbes extends RodWalker<String, String> {
else if ( vc.getType() == VariantContext.Type.MNP )
assay_sequence = leading_bases + "[" + new String(vc.getReference().getBases()) + "/" + new String(vc.getAlternateAllele(0).getBases())+"]"+trailing_bases.substring(vc.getReference().length()-1);
else if ( vc.isInsertion() )
assay_sequence = leading_bases + "[-/" + vc.getAlternateAllele(0).toString() + "]" + (char)ref.getBase() + trailing_bases;
assay_sequence = leading_bases + (char)ref.getBase() + "[-/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
else if ( vc.isDeletion() )
assay_sequence = leading_bases + "[" + new String(vc.getReference().getBases()) + "/-]" + trailing_bases.substring(vc.getReference().length()-1);
assay_sequence = leading_bases + (char)ref.getBase() + "[" + new String(vc.getReference().getBases()) + "/-]" + trailing_bases.substring(vc.getReference().length());
else
continue;