A walker that calculates read lengths, number and size of clipping events
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3327 348d0f76-0448-11de-a6fe-93d51630548a
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/*
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* Copyright (c) 2009 The Broad Institute
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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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* Þles (the ÓSoftwareÓ), 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, sub ject to the following
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* conditions:
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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 ÓAS ISÓ, 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.qc;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.DataSource;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.sam.AlignmentUtils;
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import org.broadinstitute.sting.commandline.Argument;
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import net.sf.samtools.*;
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import java.util.*;
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import java.io.File;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.io.BufferedWriter;
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/**
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* User: depristo
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* Date: May 5, 2010
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* Time: 12:16:41 PM
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*/
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/**
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* Walks over the input reads, printing out statistics about the read length, number of clipping events, and length
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* of the clipping to the output stream.
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*/
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@Requires({DataSource.READS})
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public class ReadClippingStatsWalker extends ReadWalker<ReadClippingStatsWalker.ReadClippingInfo,Integer> {
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@Argument(fullName="mappedOnly", shortName="mo", doc="when this flag is set (default), statistics will be collected "+
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"on mapped reads only, while unmapped reads will be discarded", required=false)
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protected boolean MAPPED_ONLY = true;
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@Argument(fullName="skip", shortName="skip", doc="When provided, only every skip reads are analyzed", required=false)
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protected int SKIP = 1;
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// public void initialize() {
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//
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// }
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public class ReadClippingInfo {
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SAMReadGroupRecord rg;
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int readLength, nClippingEvents, nClippedBases;
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}
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public ReadClippingInfo map(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
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if ( AlignmentUtils.isReadUnmapped(read) && MAPPED_ONLY)
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return null;
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ReadClippingInfo info = new ReadClippingInfo();
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info.rg = read.getReadGroup();
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if ( info.rg == null ) throw new StingException("Read "+read.getReadName()+" is not assigned to any read group");
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for ( CigarElement elt : read.getCigar().getCigarElements() ) {
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if ( elt.getOperator() != CigarOperator.N )
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switch ( elt.getOperator()) {
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case H : // ignore hard clips
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case S : // soft clip
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info.nClippingEvents++;
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info.nClippedBases += elt.getLength();
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// note the fall through here
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case M :
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case D : // deletion w.r.t. the reference
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case P : // ignore pads
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case I : // insertion w.r.t. the reference
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info.readLength += elt.getLength(); // Unless we have a reference skip, the read gets longer
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break;
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case N : // reference skip (looks and gets processed just like a "deletion", just different logical meaning)
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break;
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default : throw new IllegalStateException("Case statement didn't deal with cigar op: " + elt.getOperator());
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}
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}
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return info; //To change body of implemented methods use File | Settings | File Templates.
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}
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/**
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* Provide an initial value for reduce computations.
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*
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* @return Initial value of reduce.
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*/
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public Integer reduceInit() {
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out.println(Utils.join(" \t", Arrays.asList("ReadGroup", "ReadLength", "NClippingEvents", "NClippedBases", "PercentClipped")));
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return 0;
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}
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/**
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* Reduces a single map with the accumulator provided as the ReduceType.
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*
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* @param info result of the map.
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* @param sum accumulator for the reduce.
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* @return accumulator with result of the map taken into account.
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*/
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public Integer reduce(ReadClippingInfo info, Integer sum) {
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if ( info != null ) {
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if ( sum % SKIP == 0 ) {
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String id = info.rg.getReadGroupId();
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out.printf("%s\t %d\t %d\t %d\t %.2f%n",
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id, info.readLength, info.nClippingEvents, info.nClippedBases,
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100.0 * MathUtils.ratio(info.nClippedBases, info.readLength));
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}
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return sum + 1; //To change body of implemented methods use File | Settings | File Templates.
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} else {
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return sum;
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}
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}
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public void onTraversalDone(Integer result) {
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}
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}
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