103 lines
4.3 KiB
Java
Executable File
103 lines
4.3 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.VariantContext;
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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.*;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.genotype.vcf.*;
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import org.broadinstitute.sting.commandline.Argument;
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import java.util.EnumSet;
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import java.io.File;
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/**
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* Test routine for new VariantContext object
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*/
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public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
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@Argument(fullName="takeFirstOnly", doc="Only take the first second at a locus, as opposed to all", required=false)
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boolean takeFirstOnly = false;
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@Argument(fullName="onlyContextsOfType", doc="Only take variant contexts of this type", required=false)
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VariantContext.Type onlyOfThisType = null;
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@Argument(fullName="onlyContextsStartinAtCurrentPosition", doc="Only take variant contexts at actually start at the current position, excluding those at span to the current location but start earlier", required=false)
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boolean onlyContextsStartinAtCurrentPosition = false;
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@Argument(fullName="printPerLocus", doc="If true, we'll psetenv LD_LIBRARY_PATH .:/util/gcc-4.3.0/lib64:/util/gcc-4.3.0/lib/gcc/x86_64-unknown-linux-gnu/4.3.0:/util/gcc-4.3.0/lib/:/util/lib:/broad/tools/Linux/x86_64/pkgs/boost_1.38.0/lib:/humgen/gsa-scr1/GATK_Data/bwarint the variant contexts, in addition to counts", required=false)
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boolean printContexts = false;
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@Argument(fullName="outputVCF", doc="If provided, we'll convert the first input context into a VCF", required=false)
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String outputVCF = null;
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private VCFWriter writer = null;
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private boolean wroteHeader = false;
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public void initialize() {
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if ( outputVCF != null )
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writer = new VCFWriterImpl(new File(outputVCF));
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( ref == null )
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return 0;
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else {
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EnumSet<VariantContext.Type> allowedTypes = onlyOfThisType == null ? null : EnumSet.of(onlyOfThisType);
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int n = 0;
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for (VariantContext vc : tracker.getAllVariantContexts(ref, allowedTypes, context.getLocation(), onlyContextsStartinAtCurrentPosition, takeFirstOnly) ) {
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if ( writer != null && n == 0 ) {
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if ( ! wroteHeader ) {
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writer.writeHeader(VariantContextAdaptors.createVCFHeader(null, vc));
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wroteHeader = true;
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}
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writer.add(vc, ref.getBase());
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}
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n++;
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if ( printContexts ) out.printf(" %s%n", vc);
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}
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if ( n > 0 && printContexts ) {
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out.printf("%s => had %d variant context objects%n", context.getLocation(), n);
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out.printf("---------------------------------------------%n");
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}
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return n;
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}
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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 point, Integer sum) {
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return point + sum;
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}
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} |