renaming part 2...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3692 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo
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4195fc5c4e
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.vcf;
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import org.broad.tribble.vcf.VCFHeader;
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import org.broad.tribble.vcf.VCFHeaderLine;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.utils.genotype.vcf.*;
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import java.util.*;
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/**
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* Combines VCF records from different sources; supports both full merges and set unions.
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* Merge: combines multiple records into a single one; if sample names overlap then they are uniquified.
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* Union: assumes each rod represents the same set of samples (although this is not enforced); using the
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* priority list (if provided), emits a single record instance at every position represented in the rods.
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*/
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@Requires(value={})
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public class VCFCombine extends RodWalker<Integer, Integer> {
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// the types of combinations we currently allow
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public enum ComboType { UNION, MERGE }
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@Argument(fullName="combination_type", shortName="type", doc="combination type; MERGE are supported", required=true)
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protected ComboType COMBO_TYPE;
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@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)
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protected String PRIORITY_STRING = null;
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private VCFWriter vcfWriter = null;
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private List<String> priority = null;
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protected EnumSet<VariantContextUtils.MergeType> mergeOptions;
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protected final static EnumSet<VariantContextUtils.MergeType> mergeTypeOptions = EnumSet.of(VariantContextUtils.MergeType.UNION_VARIANTS, VariantContextUtils.MergeType.UNIQUIFY_GENOTYPES);
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protected final static EnumSet<VariantContextUtils.MergeType> unionTypeOptions = EnumSet.of(VariantContextUtils.MergeType.UNION_VARIANTS, VariantContextUtils.MergeType.PRIORITIZE_GENOTYPES);
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public void initialize() {
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//Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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//hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
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vcfWriter = new VCFWriter(out);
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priority = new ArrayList<String>(Arrays.asList(PRIORITY_STRING.split(",")));
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validateAnnotateUnionArguments(priority);
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mergeOptions = COMBO_TYPE == ComboType.MERGE ? mergeTypeOptions : unionTypeOptions;
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Set<String> samples = getSampleList(SampleUtils.getRodsWithVCFHeader(getToolkit(), null), mergeOptions);
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Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
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metaData.add(new VCFHeaderLine("source", "VCFCombine"));
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vcfWriter.writeHeader(new VCFHeader(metaData, samples));
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}
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private Set<String> getSampleList(Map<String, VCFHeader> headers, EnumSet<VariantContextUtils.MergeType> mergeOptions ) {
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Set<String> samples = new HashSet<String>();
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for ( Map.Entry<String, VCFHeader> val : headers.entrySet() ) {
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VCFHeader header = val.getValue();
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for ( String sample : header.getGenotypeSamples() ) {
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samples.add(VariantContextUtils.mergedSampleName(val.getKey(), sample, mergeOptions.contains(VariantContextUtils.MergeType.UNIQUIFY_GENOTYPES)));
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}
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}
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return samples;
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}
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private void validateAnnotateUnionArguments(List<String> priority) {
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Set<String> rodNames = SampleUtils.getRodsNamesWithVCFHeader(getToolkit(), null);
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if ( priority == null || rodNames.size() != priority.size() )
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throw new StingException("A complete priority list must be provided when annotateUnion is provided");
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if ( ! rodNames.containsAll(rodNames) )
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throw new StingException("Not all priority elements provided as input RODs: " + PRIORITY_STRING);
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null ) // RodWalkers can make funky map calls
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return 0;
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// get all of the vcf rods at this locus
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Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
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VariantContext mergedVC = VariantContextUtils.simpleMerge(vcs, priority, mergeOptions, true);
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if ( mergedVC != null ) // only operate at the start of events
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if ( ! mergedVC.isMixed() ) // todo remove restriction when VCF4 writer is fixed
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vcfWriter.add(mergedVC, ref.getBases());
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else
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logger.info(String.format("Ignoring complex event: " + mergedVC));
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return vcs.isEmpty() ? 0 : 1;
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}
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public Integer reduceInit() {
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return 0;
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}
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public Integer reduce(Integer counter, Integer sum) {
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return counter + sum;
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}
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public void onTraversalDone(Integer sum) {
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if ( vcfWriter != null )
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vcfWriter.close();
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}
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}
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@ -0,0 +1,88 @@
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/*
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* Copyright (c) 2010.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.vcf;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broad.tribble.vcf.VCFRecord;
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import org.broad.tribble.vcf.VCFCodec;
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import java.util.List;
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/**
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* Filters a lifted-over VCF file for ref bases that have been changed.
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*/
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@Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class))
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public class FilterLiftedVCF extends RodWalker<Integer, Integer> {
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private VCFWriter writer;
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private long failedLocs = 0, totalLocs = 0;
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public void initialize() {}
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private void filterAndWrite(char ref, VCFRecord record) {
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totalLocs++;
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char recordRef = record.getReference().charAt(0);
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if ( recordRef != ref ) {
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failedLocs++;
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} else {
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if ( writer == null ) {
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writer = new VCFWriter(out);
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writer.writeHeader(record.getHeader());
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}
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writer.addRecord(record);
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}
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return 0;
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List<Object> rods = tracker.getReferenceMetaData("vcf");
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for ( Object rod : rods )
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filterAndWrite((char)ref.getBase(), (VCFRecord)rod);
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return 0;
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}
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) { return 0; }
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public void onTraversalDone(Integer result) {
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if ( writer != null )
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writer.close();
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System.out.println("Filtered " + failedLocs + " records out of " + totalLocs + " total records.");
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}
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}
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/*
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* Copyright (c) 2010.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.vcf;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broad.tribble.vcf.VCFRecord;
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import org.broad.tribble.vcf.VCFCodec;
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import java.io.File;
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import java.util.List;
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import net.sf.picard.liftover.LiftOver;
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import net.sf.picard.util.Interval;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMFileReader;
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/**
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* Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted.
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*/
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@Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class))
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public class LiftoverVCF extends RodWalker<Integer, Integer> {
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@Argument(fullName="chain", shortName="chain", doc="Chain file", required=true)
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protected File CHAIN = null;
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@Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true)
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protected File NEW_SEQ_DICT = null;
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private VCFWriter writer;
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private LiftOver liftOver;
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private long successfulIntervals = 0, failedIntervals = 0;
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public void initialize() {
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liftOver = new LiftOver(CHAIN);
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liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH);
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final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader();
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liftOver.validateToSequences(toHeader.getSequenceDictionary());
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}
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private void convertAndWrite(VCFRecord record) {
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final Interval fromInterval = new Interval(record.getChr(), record.getStart(), record.getEnd());
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final Interval toInterval = liftOver.liftOver(fromInterval);
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if ( toInterval != null ) {
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record.setLocation(toInterval.getSequence(), toInterval.getStart());
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if ( writer == null ) {
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writer = new VCFWriter(out);
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writer.writeHeader(record.getHeader());
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}
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writer.addRecord(record);
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successfulIntervals++;
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} else {
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failedIntervals++;
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}
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return 0;
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List<Object> rods = tracker.getReferenceMetaData("vcf");
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for ( Object rod : rods )
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convertAndWrite((VCFRecord)rod);
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return 0;
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}
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) { return 0; }
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public void onTraversalDone(Integer result) {
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if ( writer != null )
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writer.close();
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System.out.println("Converted " + successfulIntervals + " records; failed to convert " + failedIntervals + " records.");
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}
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}
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