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Move to VariantContext and improve performance (and ease of use) by transitioning to be a RODWalker. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3191 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-16 20:09:48 +00:00
parent 8c32bb8f0a
commit 534f24177a
1 changed files with 23 additions and 27 deletions
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50
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.sequenom;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeatureIterator; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeatureIterator;
@ -10,12 +11,11 @@ import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.util.Arrays; import java.util.Arrays;
import java.util.Iterator; import java.util.Iterator;
import java.util.Collection;
/** /**
@ -25,7 +25,7 @@ import java.util.Iterator;
@WalkerName("PickSequenomProbes") @WalkerName("PickSequenomProbes")
@Requires(value={DataSource.REFERENCE}) @Requires(value={DataSource.REFERENCE})
@Reference(window=@Window(start=-200,stop=200)) @Reference(window=@Window(start=-200,stop=200))
public class PickSequenomProbes extends RefWalker<String, String> { public class PickSequenomProbes extends RodWalker<String, String> {
@Argument(required=false, shortName="snp_mask", doc="positions to be masked with N's") @Argument(required=false, shortName="snp_mask", doc="positions to be masked with N's")
protected String SNP_MASK = null; protected String SNP_MASK = null;
@Argument(required=false, shortName="project_id",doc="If specified, all probenames will be prepended with 'project_id|'") @Argument(required=false, shortName="project_id",doc="If specified, all probenames will be prepended with 'project_id|'")
@ -53,27 +53,24 @@ public class PickSequenomProbes extends RefWalker<String, String> {
} }
} }
public String map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) { public String map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null )
return "";
logger.debug("Probing " + ref.getLocus() + " " + ref.getWindow()); logger.debug("Probing " + ref.getLocus() + " " + ref.getWindow());
String refBase = String.valueOf(ref.getBase()); String refBase = String.valueOf(ref.getBase());
Iterator<GATKFeature> rods = rodData.getAllRods().iterator(); Collection<VariantContext> VCs = tracker.getAllVariantContexts();
Variation variant = null; if ( VCs.size() == 0 )
while (rods.hasNext()) {
Object rod = rods.next().getUnderlyingObject();
// if we have multiple variants at a locus, just take the first one we see
if ( rod instanceof Variation ) {
variant = (Variation)rod;
break;
}
}
if ( variant == null )
return ""; return "";
// if there are multiple variants at this position, just take the first one
VariantContext vc = VCs.iterator().next();
// we can only deal with biallelic sites for now
if ( !vc.isBiallelic() )
return "";
String contig = context.getLocation().getContig(); String contig = context.getLocation().getContig();
long offset = context.getLocation().getStart(); long offset = context.getLocation().getStart();
@ -100,8 +97,7 @@ public class PickSequenomProbes extends RefWalker<String, String> {
char[] context_bases = ref.getBases(); char[] context_bases = ref.getBases();
for (int i = 0; i < 401; i++) { for (int i = 0; i < 401; i++) {
GenomeLoc loc = GenomeLocParser.parseGenomeLoc(contig + ":" + true_offset + "-" + true_offset); if ( maskFlags[i] == 1 ) {
if ( maskFlags[i]==1 ) {
context_bases[i] = 'N'; context_bases[i] = 'N';
} }
true_offset += 1; true_offset += 1;
@ -110,12 +106,12 @@ public class PickSequenomProbes extends RefWalker<String, String> {
String trailing_bases = new String(Arrays.copyOfRange(context_bases, 201, 401)); String trailing_bases = new String(Arrays.copyOfRange(context_bases, 201, 401));
String assay_sequence; String assay_sequence;
if ( variant.isSNP() ) if ( vc.isSNP() )
assay_sequence = leading_bases + "[" + refBase + "/" + variant.getAlternativeBaseForSNP() + "]" + trailing_bases; assay_sequence = leading_bases + "[" + refBase + "/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
else if ( variant.isInsertion() ) else if ( vc.isInsertion() )
assay_sequence = leading_bases + refBase + "[-/" + Utils.join("",variant.getAlleleList()) + "]" + trailing_bases; assay_sequence = leading_bases + refBase + "[-/" + vc.getAlternateAllele(0).toString() + "]" + trailing_bases;
else if ( variant.isDeletion() ) else if ( vc.isDeletion() )
assay_sequence = leading_bases + refBase + "[" + Utils.join("",variant.getAlleleList()) + "/-]" + trailing_bases.substring(variant.getAlleleList().get(0).length()); assay_sequence = leading_bases + refBase + "[" + vc.getReference().toString() + "/-]" + trailing_bases.substring(vc.getReference().length());
else else
return ""; return "";
@ -130,8 +126,8 @@ public class PickSequenomProbes extends RefWalker<String, String> {
} else { } else {
assay_id.append(context.getLocation().toString().replace(':','_')); assay_id.append(context.getLocation().toString().replace(':','_'));
} }
if ( variant.isInsertion() ) assay_id.append("_gI"); if ( vc.isInsertion() ) assay_id.append("_gI");
else if ( variant.isDeletion()) assay_id.append("_gD"); else if ( vc.isDeletion()) assay_id.append("_gD");
if ( ! omitWindow ) { if ( ! omitWindow ) {
assay_id.append("_"); assay_id.append("_");