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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
This commit is contained in:
ebanks 2009-08-18 01:42:57 +00:00
parent 63d90702d6
commit 78439f7305
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -45,7 +45,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
if ( deletionBasesRemaining > 0 ) { if ( deletionBasesRemaining > 0 ) {
deletionBasesRemaining--; deletionBasesRemaining--;
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? (deletionBasesRemaining == 0 ? refBase.concat("]") : refBase) : "")); return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? (deletionBasesRemaining == 0 ? refBase.concat("/-]") : refBase) : ""));
} }
Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator(); Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator();
@ -62,13 +62,13 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
if ( indelsWriter != null ) if ( indelsWriter != null )
indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.length())); indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.length()));
// delete the next n bases, not this one // delete the next n bases, not this one
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[-/") : refBase)); return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[") : refBase));
} else if ( variant.isInsertion() ) { } else if ( variant.isInsertion() ) {
basesSeen++; basesSeen++;
if ( indelsWriter != null ) if ( indelsWriter != null )
indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.length())); indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.length()));
basesSeen += variant.length(); basesSeen += variant.length();
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(), (SEQUENOM || MASK_SNPS ? "N" : variant.getAltBasesFWD())); return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM || MASK_SNPS ? "N" : variant.getAltBasesFWD()));