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Deprecated 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5041 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-21 05:05:07 +00:00
parent c3dbbe7f91
commit 02b5d4357f
2 changed files with 0 additions and 234 deletions
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172
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
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/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFHeader;
import java.util.*;
import net.sf.samtools.SAMReadGroupRecord;
/**
* A walker that merges multiple batches of calls, by calling into the Genotyper to fill in sites that
* were called in one batch but not another.
*/
@Reference(window=@Window(start=-20,stop=20))
@By(DataSource.REFERENCE)
@Requires(value={},referenceMetaData=@RMD(name="trigger", type=VariantContext.class))
public class BatchedCallsMerger extends LocusWalker<VariantContext, Integer> implements TreeReducible<Integer> {
@ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
@Output(doc = "VCF file to which variants should be written", required = true)
public VCFWriter writer = null;
@Argument(fullName="rod_list", shortName="rods", doc="A comma-separated string describing the rod names representing individual call batches", required=true)
protected String ROD_STRING = null;
private HashSet<String> targetRods;
// the calculation arguments
private UnifiedGenotyperEngine UG_engine = null;
// mapping from rod name to set of samples coming from it
private Map<String, Set<String>> rodsToSamples = new HashMap<String, Set<String>>();
// enable deletions in the pileup
public boolean includeReadsWithDeletionAtLoci() { return true; }
// enable extended events for indels
public boolean generateExtendedEvents() { return UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.DINDEL; }
public void initialize() {
targetRods = new HashSet<String>(Arrays.asList(ROD_STRING.split(",")));
Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
// get all of the sample names and meta data
Map<String, VCFHeader> headers = VCFUtils.getVCFHeadersFromRods(getToolkit(), targetRods);
Set<String> samples = SampleUtils.getSampleList(headers);
for ( String rodName : headers.keySet() ) {
VCFHeader header = headers.get(rodName);
headerLines.addAll(header.getMetaData());
HashSet<String> mySamples = new HashSet<String>(header.getGenotypeSamples());
rodsToSamples.put(rodName, mySamples);
}
// update the engine
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples);
// initialize the header
writer.writeHeader(new VCFHeader(headerLines, samples));
}
public VariantContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null )
return null;
// get the calls at this locus
Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref, null, context.getLocation(), true, false);
Set<VariantContext> calls = new HashSet<VariantContext>();
Set<String> seenRods = new HashSet<String>();
for ( VariantContext vc : VCs ) {
if ( targetRods.contains(vc.getSource()) ) {
calls.add(vc);
seenRods.add(vc.getSource());
}
}
// if there are no calls, ignore this site
if ( seenRods.size() == 0 )
return null;
// figure out which samples still need to be called
Set<String> missedSamples = new HashSet<String>();
for ( String rod : targetRods ) {
if ( !seenRods.contains(rod) )
missedSamples.addAll(rodsToSamples.get(rod));
}
// we are missing samples, call them
if ( missedSamples.size() > 0 ) {
AlignmentContext prunedContext = filterForSamples(context.getBasePileup(), missedSamples);
VariantCallContext vcc = UG_engine.calculateLikelihoodsAndGenotypes(tracker, ref, prunedContext);
if ( vcc != null && vcc.vc != null )
calls.add(vcc.vc);
}
// merge the variant contexts
return VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), calls, ref.getBase());
}
public static AlignmentContext filterForSamples(ReadBackedPileup pileup, Set<String> samples) {
ArrayList<PileupElement> newPileup = new ArrayList<PileupElement>();
for (PileupElement p : pileup ) {
SAMReadGroupRecord readGroup = p.getRead().getReadGroup();
if ( readGroup != null && samples.contains(readGroup.getSample()) )
newPileup.add(p);
}
return new AlignmentContext(pileup.getLocation(), new ReadBackedPileupImpl(pileup.getLocation(), newPileup));
}
public Integer reduceInit() { return 0; }
public Integer treeReduce(Integer lhs, Integer rhs) {
return lhs + rhs;
}
public Integer reduce(VariantContext value, Integer sum) {
// can't call the locus because of no coverage or no confidence
if ( value == null )
return sum;
try {
writer.add(value, value.getReference().getBases()[0]);
} catch (IllegalArgumentException e) {
throw new IllegalArgumentException(e.getMessage() + "; this is often caused by using the --assume_single_sample_reads argument with the wrong sample name");
}
return sum;
}
public void onTraversalDone(Integer sum) {}
}

62
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/CreateTriggerTrack.java
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@ -1,62 +0,0 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.commandline.Output;
import java.util.Collection;
import java.io.PrintWriter;
/**
* Creates a bed-format trigger-track for the Unified Genotyper based on input variant files.
*/
public class CreateTriggerTrack extends RodWalker<Integer, Integer> {
@Output
private PrintWriter writer;
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null )
return 0;
Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref);
if ( VCs.size() > 0 )
writer.println(context.getLocation().getContig() + "\t" + (context.getLocation().getStart()-1) + "\t" + context.getLocation().getStart());
return 0;
}
public Integer reduceInit() { return 0; }
public Integer reduce(Integer value, Integer sum) { return 0; }
public void onTraversalDone(Integer result) {
writer.close();
}
}