From 78439f73057aa03945bdea6423b390417dce6b03 Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 18 Aug 2009 01:42:57 +0000 Subject: [PATCH] Modify Sequenom input format based on official documentation git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1430 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/fasta/FastaAlternateReferenceWalker.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index 7c71a4bda..35c8445e3 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java @@ -45,7 +45,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker { if ( deletionBasesRemaining > 0 ) { deletionBasesRemaining--; - return new Pair(context.getLocation(), (SEQUENOM ? (deletionBasesRemaining == 0 ? refBase.concat("]") : refBase) : "")); + return new Pair(context.getLocation(), (SEQUENOM ? (deletionBasesRemaining == 0 ? refBase.concat("/-]") : refBase) : "")); } Iterator rods = rodData.getAllRods().iterator(); @@ -62,13 +62,13 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker { if ( indelsWriter != null ) indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.length())); // delete the next n bases, not this one - return new Pair(context.getLocation(), (SEQUENOM ? refBase.concat("[-/") : refBase)); + return new Pair(context.getLocation(), (SEQUENOM ? refBase.concat("[") : refBase)); } else if ( variant.isInsertion() ) { basesSeen++; if ( indelsWriter != null ) indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.length())); basesSeen += variant.length(); - return new Pair(context.getLocation(), (SEQUENOM ? refBase.concat("[+/"+variant.getAltBasesFWD()+"]") : refBase.concat(variant.getAltBasesFWD()))); + return new Pair(context.getLocation(), (SEQUENOM ? refBase.concat("[-/"+variant.getAltBasesFWD()+"]") : refBase.concat(variant.getAltBasesFWD()))); } else if ( variant.isSNP() ) { basesSeen++; return new Pair(context.getLocation(), (SEQUENOM || MASK_SNPS ? "N" : variant.getAltBasesFWD()));