From ac3fd567b416f39fe40fd7fc107087c37e55e034 Mon Sep 17 00:00:00 2001 From: asivache Date: Fri, 28 Jan 2011 02:53:03 +0000 Subject: [PATCH] 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 --- .../sting/gatk/walkers/sequenom/PickSequenomProbes.java | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java index 81c45206b..a5afd30c3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java @@ -120,6 +120,11 @@ public class PickSequenomProbes extends RodWalker { 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 { 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;