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deleting vcf 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3693 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-06-30 20:19:15 +00:00
parent 4195fc5c4e
commit aa20c52b88
3 changed files with 0 additions and 331 deletions
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133
java/src/org/broadinstitute/sting/gatk/walkers/vcf/CombineVariants.java
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@ -1,133 +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.vcf;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.genotype.vcf.*;
import java.util.*;
/**
* Combines VCF records from different sources; supports both full merges and set unions.
* Merge: combines multiple records into a single one; if sample names overlap then they are uniquified.
* Union: assumes each rod represents the same set of samples (although this is not enforced); using the
* priority list (if provided), emits a single record instance at every position represented in the rods.
*/
@Requires(value={})
public class VCFCombine extends RodWalker<Integer, Integer> {
// the types of combinations we currently allow
public enum ComboType { UNION, MERGE }
@Argument(fullName="combination_type", shortName="type", doc="combination type; MERGE are supported", required=true)
protected ComboType COMBO_TYPE;
@Argument(fullName="rod_priority_list", shortName="priority", doc="When taking the union of variants containing genotypes: a comma-separated string describing the priority ordering for the genotypes as far as which record gets emitted; a complete priority list MUST be provided", required=true)
protected String PRIORITY_STRING = null;
private VCFWriter vcfWriter = null;
private List<String> priority = null;
protected EnumSet<VariantContextUtils.MergeType> mergeOptions;
protected final static EnumSet<VariantContextUtils.MergeType> mergeTypeOptions = EnumSet.of(VariantContextUtils.MergeType.UNION_VARIANTS, VariantContextUtils.MergeType.UNIQUIFY_GENOTYPES);
protected final static EnumSet<VariantContextUtils.MergeType> unionTypeOptions = EnumSet.of(VariantContextUtils.MergeType.UNION_VARIANTS, VariantContextUtils.MergeType.PRIORITIZE_GENOTYPES);
public void initialize() {
//Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
//hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
vcfWriter = new VCFWriter(out);
priority = new ArrayList<String>(Arrays.asList(PRIORITY_STRING.split(",")));
validateAnnotateUnionArguments(priority);
mergeOptions = COMBO_TYPE == ComboType.MERGE ? mergeTypeOptions : unionTypeOptions;
Set<String> samples = getSampleList(SampleUtils.getRodsWithVCFHeader(getToolkit(), null), mergeOptions);
Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
metaData.add(new VCFHeaderLine("source", "VCFCombine"));
vcfWriter.writeHeader(new VCFHeader(metaData, samples));
}
private Set<String> getSampleList(Map<String, VCFHeader> headers, EnumSet<VariantContextUtils.MergeType> mergeOptions ) {
Set<String> samples = new HashSet<String>();
for ( Map.Entry<String, VCFHeader> val : headers.entrySet() ) {
VCFHeader header = val.getValue();
for ( String sample : header.getGenotypeSamples() ) {
samples.add(VariantContextUtils.mergedSampleName(val.getKey(), sample, mergeOptions.contains(VariantContextUtils.MergeType.UNIQUIFY_GENOTYPES)));
}
}
return samples;
}
private void validateAnnotateUnionArguments(List<String> priority) {
Set<String> rodNames = SampleUtils.getRodsNamesWithVCFHeader(getToolkit(), null);
if ( priority == null || rodNames.size() != priority.size() )
throw new StingException("A complete priority list must be provided when annotateUnion is provided");
if ( ! rodNames.containsAll(rodNames) )
throw new StingException("Not all priority elements provided as input RODs: " + PRIORITY_STRING);
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null ) // RodWalkers can make funky map calls
return 0;
// get all of the vcf rods at this locus
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
VariantContext mergedVC = VariantContextUtils.simpleMerge(vcs, priority, mergeOptions, true);
if ( mergedVC != null ) // only operate at the start of events
if ( ! mergedVC.isMixed() ) // todo remove restriction when VCF4 writer is fixed
vcfWriter.add(mergedVC, ref.getBases());
else
logger.info(String.format("Ignoring complex event: " + mergedVC));
return vcs.isEmpty() ? 0 : 1;
}
public Integer reduceInit() {
return 0;
}
public Integer reduce(Integer counter, Integer sum) {
return counter + sum;
}
public void onTraversalDone(Integer sum) {
if ( vcfWriter != null )
vcfWriter.close();
}
}

88
java/src/org/broadinstitute/sting/gatk/walkers/vcf/FilterLiftedVCF.java
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@ -1,88 +0,0 @@
/*
* Copyright (c) 2010.
*
* 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.vcf;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
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.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFCodec;
import java.util.List;
/**
* Filters a lifted-over VCF file for ref bases that have been changed.
*/
@Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class))
public class FilterLiftedVCF extends RodWalker<Integer, Integer> {
private VCFWriter writer;
private long failedLocs = 0, totalLocs = 0;
public void initialize() {}
private void filterAndWrite(char ref, VCFRecord record) {
totalLocs++;
char recordRef = record.getReference().charAt(0);
if ( recordRef != ref ) {
failedLocs++;
} else {
if ( writer == null ) {
writer = new VCFWriter(out);
writer.writeHeader(record.getHeader());
}
writer.addRecord(record);
}
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null )
return 0;
List<Object> rods = tracker.getReferenceMetaData("vcf");
for ( Object rod : rods )
filterAndWrite((char)ref.getBase(), (VCFRecord)rod);
return 0;
}
public Integer reduceInit() { return 0; }
public Integer reduce(Integer value, Integer sum) { return 0; }
public void onTraversalDone(Integer result) {
if ( writer != null )
writer.close();
System.out.println("Filtered " + failedLocs + " records out of " + totalLocs + " total records.");
}
}

110
java/src/org/broadinstitute/sting/gatk/walkers/vcf/LiftoverVCF.java
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@ -1,110 +0,0 @@
/*
* Copyright (c) 2010.
*
* 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.vcf;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
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.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFCodec;
import java.io.File;
import java.util.List;
import net.sf.picard.liftover.LiftOver;
import net.sf.picard.util.Interval;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
/**
* Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted.
*/
@Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class))
public class LiftoverVCF extends RodWalker<Integer, Integer> {
@Argument(fullName="chain", shortName="chain", doc="Chain file", required=true)
protected File CHAIN = null;
@Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true)
protected File NEW_SEQ_DICT = null;
private VCFWriter writer;
private LiftOver liftOver;
private long successfulIntervals = 0, failedIntervals = 0;
public void initialize() {
liftOver = new LiftOver(CHAIN);
liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH);
final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader();
liftOver.validateToSequences(toHeader.getSequenceDictionary());
}
private void convertAndWrite(VCFRecord record) {
final Interval fromInterval = new Interval(record.getChr(), record.getStart(), record.getEnd());
final Interval toInterval = liftOver.liftOver(fromInterval);
if ( toInterval != null ) {
record.setLocation(toInterval.getSequence(), toInterval.getStart());
if ( writer == null ) {
writer = new VCFWriter(out);
writer.writeHeader(record.getHeader());
}
writer.addRecord(record);
successfulIntervals++;
} else {
failedIntervals++;
}
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null )
return 0;
List<Object> rods = tracker.getReferenceMetaData("vcf");
for ( Object rod : rods )
convertAndWrite((VCFRecord)rod);
return 0;
}
public Integer reduceInit() { return 0; }
public Integer reduce(Integer value, Integer sum) { return 0; }
public void onTraversalDone(Integer result) {
if ( writer != null )
writer.close();
System.out.println("Converted " + successfulIntervals + " records; failed to convert " + failedIntervals + " records.");
}
}