86 lines
3.3 KiB
Java
Executable File
86 lines
3.3 KiB
Java
Executable File
/*
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* Copyright (c) 2009 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 THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.contexts;
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import org.broadinstitute.sting.gatk.refdata.RodGeliText;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.RodVCF;
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import net.sf.samtools.SAMRecord;
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import java.util.*;
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public class VariantContext {
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private RefMetaDataTracker tracker;
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private ReferenceContext ref;
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private AlignmentContext context;
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private RodGeliText variant;
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private RodVCF variantVCF;
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private AlignmentContext Q0freeContext = null;
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public VariantContext(RefMetaDataTracker tracker, ReferenceContext ref,
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AlignmentContext context, RodGeliText variant, RodVCF variantVCF) {
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this.tracker = tracker;
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this.ref = ref;
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this.context = context;
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this.variant = variant;
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this.variantVCF = variantVCF;
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}
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public RefMetaDataTracker getTracker() { return tracker; }
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public ReferenceContext getReferenceContext() { return ref; }
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public RodGeliText getVariant() { return variant; }
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public RodVCF getVariantVCF() { return variantVCF; }
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public AlignmentContext getAlignmentContext(boolean useMQ0Reads) {
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return (useMQ0Reads ? context : getQ0freeContext());
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}
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private AlignmentContext getQ0freeContext() {
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if ( Q0freeContext == null ) {
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// set up the variables
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List<SAMRecord> reads = context.getReads();
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List<Integer> offsets = context.getOffsets();
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Iterator<SAMRecord> readIter = reads.iterator();
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Iterator<Integer> offsetIter = offsets.iterator();
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ArrayList<SAMRecord> Q0freeReads = new ArrayList<SAMRecord>();
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ArrayList<Integer> Q0freeOffsets = new ArrayList<Integer>();
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// copy over good reads/offsets
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while ( readIter.hasNext() ) {
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SAMRecord read = readIter.next();
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Integer offset = offsetIter.next();
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if ( read.getMappingQuality() > 0 ) {
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Q0freeReads.add(read);
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Q0freeOffsets.add(offset);
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}
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}
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Q0freeContext = new AlignmentContext(context.getLocation(), Q0freeReads, Q0freeOffsets);
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}
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return Q0freeContext;
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}
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} |