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Archiving CoverageBySample 

This walker was not updated since 2009, and users were getting wrong answers when running it with ReduceReads. I don't want to deal with this because DiagnoseTargets does everything this walker does.
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Mauricio Carneiro 2013-02-26 13:49:00 -05:00
parent 51d618de97
commit 711cbd3b5a
1 changed files with 0 additions and 108 deletions
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public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
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/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.examples;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.io.PrintStream;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
/**
* Computes the coverage per sample for every position (use with -L argument!).
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class CoverageBySample extends LocusWalker<Integer, Integer> {
@Output
protected PrintStream out;
private HashSet<String> sampleNames = new HashSet<String>();
public boolean requiresReads() { return true; }
public void initialize() {
List<SAMReadGroupRecord> read_groups = this.getToolkit().getSAMFileHeader().getReadGroups();
for ( SAMReadGroupRecord record : read_groups ) {
String sample = record.getSample();
if ( sample != null )
sampleNames.add(sample);
}
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
HashMap<String, Integer> depthBySample = new HashMap<String, Integer>();
for ( String sample : sampleNames )
depthBySample.put(sample, 0);
ReadBackedPileup pileup = context.getPileup();
for ( PileupElement p : pileup ) {
SAMReadGroupRecord readGroup = p.getRead().getReadGroup();
if ( readGroup == null )
continue;
String sample = readGroup.getSample();
if ( sample != null ) {
int oldDepth = depthBySample.get(sample);
depthBySample.put(sample, oldDepth + 1);
}
}
for ( Map.Entry<String, Integer> sample : depthBySample.entrySet() ) {
out.printf(" %s %8d%n", sample.getKey(), sample.getValue());
}
return 1;
}
public void onTraversalDone(Integer result) {
out.println("Processed " + result + " loci.");
}
public Integer reduceInit() {
return 0;
}
public Integer reduce(Integer value, Integer sum) {
return sum + value;
}
}