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output correct format for Sequenom SNPs 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1567 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-09 19:21:53 +00:00
parent 43d1c6741c
commit 542af6402e
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -66,7 +66,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[-/"+variant.getAltBasesFWD()+"]") : refBase.concat(variant.getAltBasesFWD()))); return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[-/"+variant.getAltBasesFWD()+"]") : refBase.concat(variant.getAltBasesFWD())));
} else if ( variant.isSNP() ) { } else if ( variant.isSNP() ) {
basesSeen++; basesSeen++;
return new Pair<GenomeLoc, String>(context.getLocation(), (rod.getName().startsWith("snpmask") ? "N" : variant.getAltBasesFWD())); return new Pair<GenomeLoc, String>(context.getLocation(), (rod.getName().startsWith("snpmask") ? "N" : ("[" + refBase + "/" + variant.getAltBasesFWD() + "]")));
} }
} }