221 lines
8.0 KiB
Java
Executable File
221 lines
8.0 KiB
Java
Executable File
/*
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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.oneoffprojects.walkers;
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import org.broad.tribble.util.variantcontext.Allele;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.VCFConstants;
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import org.broadinstitute.sting.commandline.Argument;
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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.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.StingException;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input VCF file
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* @help.summary Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input VCF file
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*/
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//@Requires(value={},referenceMetaData=@RMD(name=BeagleOutputByDepthWalker.INPUT_EVAL_ROD_NAME,type= VCFRecord.class))
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public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
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public static final String POSTBEAGLE_EVAL_ROD_NAME = "postbeaglevcf";
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public static final String PREBEAGLE_EVAL_ROD_NAME = "prebeaglevcf";
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public static final String INPUT_HAPMAP_ROD_NAME = "hapmap";
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public static final String INPUT_COMP_ROD_NAME = "comp";
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private boolean newLine = true;
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@Argument(fullName = "output_file", shortName = "output", doc = "File to output results", required = true)
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public PrintStream outputWriter = null;
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public void initialize() {
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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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GenomeLoc loc = context.getLocation();
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VariantContext vc_postbgl = tracker.getVariantContext(ref,POSTBEAGLE_EVAL_ROD_NAME, null, loc, false);
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VariantContext vc_prebgl = tracker.getVariantContext(ref,PREBEAGLE_EVAL_ROD_NAME, null, loc, false);
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VariantContext vc_hapmap = tracker.getVariantContext(ref,INPUT_HAPMAP_ROD_NAME, null, loc, false);
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VariantContext vc_comp = tracker.getVariantContext(ref,INPUT_COMP_ROD_NAME, null, loc, false);
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if ( vc_postbgl == null || vc_prebgl == null || vc_comp == null)
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return 0;
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if (!vc_prebgl.hasGenotypes() || !vc_postbgl.hasGenotypes() )
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return 0;
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if (vc_postbgl.isFiltered())
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return 0;
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Map<String, Genotype> compGenotypes = vc_comp.getGenotypes();
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Integer alleleCountH = 0, chrCountH = 0, alleleCountEmp=0, chrCountEmp=0;
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// Get Hapmap AC and AF
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if (vc_hapmap != null) {
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Map<String, Genotype> hapmapGenotypes = vc_hapmap.getGenotypes();
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for ( String sample : vc_postbgl.getSampleNames() ) {
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// use sample as key into genotypes structure
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if (vc_postbgl.getGenotypes().containsKey(sample) && hapmapGenotypes.containsKey(sample)) {
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Genotype hapmapGenotype = hapmapGenotypes.get(sample);
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if (hapmapGenotype.isCalled()){
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chrCountH += 2;
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if (hapmapGenotype.isHet()) {
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alleleCountH += 1;
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} else if (hapmapGenotype.isHomVar()) {
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alleleCountH += 2;
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}
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}
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}
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}
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}
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else {
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alleleCountH = -1;
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chrCountH = -1;
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}
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chrCountEmp = vc_postbgl.getChromosomeCount();
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//System.out.println(chrCountH);
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if ( vc_postbgl.getAlternateAlleles().size() > 0 ) {
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for ( Allele allele : vc_postbgl.getAlternateAlleles() ) {
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alleleCountEmp = alleleCountEmp+vc_postbgl.getChromosomeCount(allele);
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}
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//System.out.println(alleleCountH);
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}
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for ( String sample : vc_postbgl.getSampleNames() ) {
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if (sample.compareToIgnoreCase("NA12878")!=0)
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continue;
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// use sample as key into genotypes structure
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Genotype postbglGenotype = vc_postbgl.getGenotype(sample);
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Genotype prebglGenotype = vc_prebgl.getGenotype(sample);
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Genotype compGenotype = compGenotypes.get(sample);
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outputWriter.format("%d %d %d %d %d ", vc_postbgl.getStart(), alleleCountH, chrCountH,
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alleleCountEmp, chrCountEmp);
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String dps = postbglGenotype.getAttributeAsString(VCFConstants.DEPTH_KEY);
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int dp;
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if (dps.compareTo(".")==0)
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dp = -1;
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else
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dp = Integer.valueOf(dps);
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int hg, bg, pg;
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if (compGenotype.isNoCall())
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hg = -1;
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else if (compGenotype.isHomRef())
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hg = 0;
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else if (compGenotype.isHet())
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hg = 1;
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else if (compGenotype.isHomVar())
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hg = 2;
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else
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throw new StingException("Bug! invalid genotype!");
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if (postbglGenotype.isNoCall())
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bg = -1;
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else if (postbglGenotype.isHomRef())
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bg = 0;
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else if (postbglGenotype.isHet())
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bg = 1;
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else if (postbglGenotype.isHomVar())
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bg = 2;
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else
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throw new StingException("Bug! invalid genotype!");
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if (prebglGenotype.isNoCall())
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pg = -1;
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else if (prebglGenotype.isHomRef())
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pg = 0;
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else if (prebglGenotype.isHet())
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pg = 1;
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else if (prebglGenotype.isHomVar())
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pg = 2;
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else
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throw new StingException("Bug! invalid genotype!");
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outputWriter.format("%d %d %d %d\n",dp, hg, pg, bg);
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}
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return 1;
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}
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return 0;
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}
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public Integer reduceInit() {
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return 0; // Nothing to do here
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}
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/**
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* Increment the number of loci processed.
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*
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* @param value result of the map.
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* @param sum accumulator for the reduce.
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* @return the new number of loci processed.
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*/
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public Integer reduce(Integer value, Integer sum) {
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return sum + value;
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}
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/**
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* Tell the user the number of loci processed and close out the new variants file.
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*
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* @param result the number of loci seen.
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*/
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public void onTraversalDone(Integer result) {
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out.printf("Processed %d loci.\n", result);
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}
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}
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