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Fix for Kris: now SNPs aren't masked by default (only when they come from a mask rod) and we can design Sequenom validation assays for them. 

I'll move this all to core in a bit...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1532 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-04 14:52:06 +00:00
parent 849dce799d
commit 42c71b4382
1 changed files with 4 additions and 9 deletions
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13
java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -11,18 +11,13 @@ import java.io.*;
import java.util.Iterator; import java.util.Iterator;
// create a fasta sequence file from a reference, intervals, and rod(s) of variants
// if there are multiple variants at a site, we take the first one seen
@WalkerName("FastaAlternateReferenceMaker") @WalkerName("FastaAlternateReferenceMaker")
@Requires(value={DataSource.REFERENCE}) @Requires(value={DataSource.REFERENCE})
public class FastaAlternateReferenceWalker extends FastaReferenceWalker { public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
@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) @Argument(fullName="outputSequenomFormat", shortName="sequenom", doc="output results in sequenom format (overrides 'maskSNPs' argument)", required=false)
private Boolean SEQUENOM = false; private Boolean SEQUENOM = false;
@Argument(fullName="outputIndelPositions", shortName="indels", doc="output the positions of the indels in the new reference", required=false) @Argument(fullName="outputIndelPositions", shortName="indelPositions", doc="output the positions of the indels in the new reference", required=false)
String indelsFile = null; String indelsFile = null;
private int deletionBasesRemaining = 0; private int deletionBasesRemaining = 0;
@ -56,14 +51,14 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
// if we have multiple variants at a locus, just take the first damn one we see for now // if we have multiple variants at a locus, just take the first damn one we see for now
AllelicVariant variant = (AllelicVariant)rod; AllelicVariant variant = (AllelicVariant)rod;
if ( ! rod.getName().equals("snpmask") && variant.isDeletion() ) { if ( !rod.getName().startsWith("snpmask") && variant.isDeletion() ) {
deletionBasesRemaining = variant.length(); deletionBasesRemaining = variant.length();
basesSeen++; basesSeen++;
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 ( ! rod.getName().equals("snpmask") && variant.isInsertion() ) { } else if ( !rod.getName().startsWith("snpmask") && 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()));
@ -71,7 +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(), (SEQUENOM || MASK_SNPS ? "N" : variant.getAltBasesFWD())); return new Pair<GenomeLoc, String>(context.getLocation(), (rod.getName().startsWith("snpmask") ? "N" : variant.getAltBasesFWD()));
} }
} }