A succint walker that reports GC content by interval. Taking down two old implementations of the same thing from oneoffs. Documentation added to the wiki.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5790 348d0f76-0448-11de-a6fe-93d51630548a
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/*
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* Copyright (c) 2011, 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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* 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.walkers;
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import org.broadinstitute.sting.commandline.Output;
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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.*;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.collections.Pair;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* Walks along reference and calculates the GC content for each interval.
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*/
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@Allows(value = {DataSource.REFERENCE})
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@Requires(value = {DataSource.REFERENCE})
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@By(DataSource.REFERENCE)
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public class GCContentByIntervalWalker extends LocusWalker<Long, Long> {
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@Output
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protected PrintStream out;
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public boolean isReduceByInterval() {
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return true;
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}
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public void initialize() {
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}
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public boolean generateExtendedEvents() {
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return false;
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}
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public Long reduceInit() {
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return 0L;
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}
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public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (tracker == null)
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return null;
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int baseIndex = ref.getBaseIndex();
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return (baseIndex == BaseUtils.gIndex || baseIndex == BaseUtils.cIndex) ? 1L : 0L;
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}
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public Long reduce(Long toAdd, Long runningCount) {
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return runningCount + toAdd;
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}
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public void onTraversalDone(List<Pair<GenomeLoc, Long>> results) {
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for (Pair<GenomeLoc, Long> result : results ) {
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GenomeLoc loc = result.getFirst();
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Long gcCount = result.getSecond();
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double gcContent = (double) gcCount / loc.size();
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out.println(loc + "\t" + gcContent);
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}
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}
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}
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@ -1,134 +0,0 @@
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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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* 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.oneoffprojects.walkers.CNV;
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import org.broadinstitute.sting.commandline.Output;
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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.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* Walks along reference and calculates the GC content for each interval.
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*/
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@Allows(value = {DataSource.REFERENCE})
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@Requires(value = {DataSource.REFERENCE})
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@By(DataSource.REFERENCE)
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public class GCcontentIntervalWalker extends LocusWalker<GCcounter, GCcounter> {
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@Output
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protected PrintStream out;
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public boolean isReduceByInterval() {
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return true;
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}
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public void initialize() {
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}
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public boolean generateExtendedEvents() {
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return false;
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}
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public GCcounter reduceInit() {
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return new GCcounter();
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}
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/**
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* @param tracker the meta-data tracker
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* @param ref the reference base
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* @param context the context for the given locus
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* @return statistics of and list of all phased VariantContexts and their base pileup that have gone out of cacheWindow range.
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*/
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public GCcounter map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (tracker == null)
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return null;
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return new GCcounter().calculateGCandAddIn(ref);
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}
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public GCcounter reduce(GCcounter add, GCcounter runningCount) {
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if (add == null)
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add = new GCcounter();
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return runningCount.addIn(add);
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}
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/**
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* @param results the GC content observed for each interval.
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*/
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public void onTraversalDone(List<Pair<GenomeLoc, GCcounter>> results) {
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for (Pair<GenomeLoc, GCcounter> result : results ) {
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GenomeLoc loc = result.getFirst();
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GCcounter counter = result.getSecond();
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double gcContent = (double) counter.GCcount / counter.totalCount;
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out.println(loc + "\t" + gcContent + "\t" + loc.size());
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}
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}
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}
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class GCcounter {
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public int totalCount;
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public int GCcount;
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public GCcounter() {
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this.totalCount = 0;
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this.GCcount = 0;
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}
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public GCcounter addIn(GCcounter other) {
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this.totalCount += other.totalCount;
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this.GCcount += other.GCcount;
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return this;
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}
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public GCcounter calculateGCandAddIn(ReferenceContext ref) {
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for (byte base : ref.getBases()) {
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int baseIndex = BaseUtils.simpleBaseToBaseIndex(base);
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boolean baseIsGC = (baseIndex == BaseUtils.gIndex || baseIndex == BaseUtils.cIndex);
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boolean baseIsAT = (baseIndex == BaseUtils.aIndex || baseIndex == BaseUtils.tIndex);
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if (baseIsGC || baseIsAT) {
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totalCount++;
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if (baseIsGC)
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GCcount++;
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}
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}
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return this;
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}
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}
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@ -1,71 +0,0 @@
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package org.broadinstitute.sting.oneoffprojects.walkers;
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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.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.walkers.RefWalker;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.commandline.Output;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import java.io.PrintStream;
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/**
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* IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
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*
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* @Author chartl
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* @Date May 19, 2010
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*/
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public class GCCalculatorWalker extends RefWalker<Pair<Set<GenomeLoc>,Boolean>, Map<GenomeLoc,Pair<Long,Long>>> {
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@Output
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PrintStream out;
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public Map<GenomeLoc,Pair<Long,Long>> reduceInit() {
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return new HashMap<GenomeLoc,Pair<Long,Long>>();
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}
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public Pair<Set<GenomeLoc>,Boolean> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null || tracker.getReferenceMetaData("interval_list") == null ) {
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return null;
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} else {
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Set<GenomeLoc> overlappingIntervals = new HashSet<GenomeLoc>();
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for ( GATKFeature f : tracker.getGATKFeatureMetaData("interval_list",true) ) {
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overlappingIntervals.add( f.getLocation() );
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}
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return new Pair<Set<GenomeLoc>,Boolean>(overlappingIntervals, ref.getBaseIndex() == BaseUtils.cIndex || ref.getBaseIndex() == BaseUtils.gIndex );
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}
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}
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public Map<GenomeLoc,Pair<Long,Long>> reduce(Pair<Set<GenomeLoc>,Boolean> map, Map<GenomeLoc,Pair<Long,Long>> prevReduce) {
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if ( map == null ) {
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return prevReduce;
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}
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for ( GenomeLoc loc : map.first ) {
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if ( ! prevReduce.keySet().contains(loc) ) {
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prevReduce.put(loc,new Pair<Long,Long>(0l,0l));
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}
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prevReduce.get(loc).first ++;
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if ( map.second ) {
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prevReduce.get(loc).second ++;
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}
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}
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return prevReduce;
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}
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public void onTraversalDone(Map<GenomeLoc,Pair<Long,Long>> reduced ) {
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for ( Map.Entry<GenomeLoc,Pair<Long,Long>> gcCounts : reduced.entrySet() ) {
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double gc_content = ( (double) gcCounts.getValue().second )/( (double) gcCounts.getValue().first );
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out.printf("%s\t%.2f%n",gcCounts.getKey().toString(),100*gc_content);
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}
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}
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}
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