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option to output in sequenom input format 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1415 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-12 16:50:37 +00:00
parent 7f1159b6a9
commit 143f8eea4e
1 changed files with 9 additions and 8 deletions
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17
java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -18,14 +18,18 @@ public class FastaAlternateReferenceWalker extends RefWalker<Pair<GenomeLoc, Str
@Argument(fullName="maskSNPs", shortName="mask", doc="print 'N' at SNP sites instead of the alternate allele", required=false)
private Boolean MASK_SNPS = false;
@Argument(fullName="outputSequenomFormat", shortName="sequenom", doc="output results in sequenom format (overrides 'maskSNPs' argument)", required=false)
private Boolean SEQUENOM = false;
private StringBuffer sb = new StringBuffer();
int deletionBasesRemaining = 0;
public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
String refBase = String.valueOf(ref.getBase());
if ( deletionBasesRemaining > 0 ) {
deletionBasesRemaining--;
return new Pair<GenomeLoc, String>(context.getLocation(), "");
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? (deletionBasesRemaining == 0 ? refBase.concat("]") : refBase) : ""));
}
Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator();
@ -39,19 +43,16 @@ public class FastaAlternateReferenceWalker extends RefWalker<Pair<GenomeLoc, Str
if ( variant.isDeletion() ) {
deletionBasesRemaining = variant.length();
// delete the next n bases, not this one
return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf(ref.getBase()));
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[-/") : refBase));
} else if ( variant.isInsertion() ) {
return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf(ref.getBase()).concat(variant.getAltBasesFWD()));
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[+/"+variant.getAltBasesFWD()+"]") : refBase.concat(variant.getAltBasesFWD())));
} else if ( variant.isSNP() ) {
if ( MASK_SNPS )
return new Pair<GenomeLoc, String>(context.getLocation(), "N");
else
return new Pair<GenomeLoc, String>(context.getLocation(), variant.getAltBasesFWD());
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM || MASK_SNPS ? "N" : variant.getAltBasesFWD()));
}
}
// if we got here then we're just ref
return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf(ref.getBase()));
return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
}
public Pair<GenomeLoc, String> reduceInit() {