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Cleanup pileup and depth of coverage in preparation for release. Add pileup, depth of coverage, and print reads to package for distribution. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1159 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-02 14:54:01 +00:00
parent 6a25f0b9c5
commit 62807139fc
3 changed files with 107 additions and 53 deletions
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36
java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
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@ -1,18 +1,36 @@
/*
* Copyright (c) 2009 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.walkers;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.Pair;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: mdepristo
* Date: Feb 22, 2009
* Time: 3:22:14 PM
* To change this template use File | Settings | File Templates.
* Display the depth of coverage at a given locus.
*/
public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>> {
@Argument(fullName="suppressLocusPrinting",doc="Suppress printing",required=false)
@ -28,12 +46,12 @@ public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>
return true;
}
public Pair<Long, Long> reduceInit() { return new Pair(0l,0l); }
public Pair<Long, Long> reduceInit() { return new Pair<Long,Long>(0l,0l); }
public Pair<Long, Long> reduce(Integer value, Pair<Long, Long> sum) {
long left = value.longValue() + sum.getFirst();
long right = sum.getSecond() + 1l;
return new Pair(left, right);
return new Pair<Long,Long>(left, right);
}
public void onTraversalDone(Pair<Long, Long> result) {

121
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
View File

@ -1,3 +1,27 @@
/*
* Copyright (c) 2009 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.walkers;
import org.broadinstitute.sting.gatk.LocusContext;
@ -7,9 +31,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.Utils;
import net.sf.samtools.SAMRecord;
import java.util.List;
/**
* samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
@ -32,16 +53,14 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
@Argument(fullName="alwaysShowSecondBase",doc="If true, prints dummy bases for the second bases in the BAM file where they are missing",required=false)
public boolean alwaysShowSecondBase = false;
//@Argument(fullName="showSecondBaseQuals",doc="If true, prints out second base qualities in the pileup",required=false)
//public boolean showSecondBaseQuals = false;
@Argument(fullName="qualsAsInts",doc="If true, prints out qualities in the pileup as comma-separated integers",required=false)
public boolean qualsAsInts = false;
@Argument(fullName="extended",shortName="ext",doc="extended",required=false)
public boolean EXTENDED = false;
public boolean FLAG_UNCOVERED_BASES = true; // todo: how do I make this a command line argument?
@Argument(fullName="ignore_uncovered_bases",shortName="skip_uncov",doc="Output nothing when a base is uncovered")
public boolean IGNORE_UNCOVERED_BASES = false;
public void initialize() {
}
@ -50,47 +69,16 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
String bases = pileup.getBases();
if ( bases.equals("") && FLAG_UNCOVERED_BASES ) {
if ( bases.equals("") && !IGNORE_UNCOVERED_BASES ) {
bases = "***UNCOVERED_SITE***";
}
StringBuilder extras = new StringBuilder();
String secondBasePileup = "";
if(shouldShowSecondaryBasePileup(pileup))
secondBasePileup = getSecondBasePileup(pileup);
String rods = getReferenceOrderedData( tracker );
String secondBasePileup = pileup.getSecondaryBasePileup();
if ( secondBasePileup == null && alwaysShowSecondBase ) {
secondBasePileup = Utils.dupString('N', bases.length());
}
if ( secondBasePileup != null ) extras.append(" ").append(secondBasePileup);
/*
if ( showSecondBaseQuals ) {
String secondQualPileup = pileup.getSecondaryQualPileup();
if ( secondQualPileup == null )
secondQualPileup = Utils.dupString((char)(33), bases.length());
extras.append(" ").append(secondQualPileup);
}
*/
String rodString = "";
for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {
if ( datum != null && ! (datum instanceof rodDbSNP)) {
//System.out.printf("rod = %s%n", datum.toSimpleString());
rodString += datum.toSimpleString();
//System.out.printf("Rod string %s%n", rodString);
}
}
rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null);
if ( dbsnp != null )
rodString += dbsnp.toMediumString();
if ( rodString != "" )
rodString = "[ROD: " + rodString + "]";
//if ( context.getLocation().getStart() % 1 == 0 ) {
//System.out.printf("quals as ints %b%n", qualsAsInts);
out.printf("%s%s %s%n", pileup.getPileupString(qualsAsInts), extras, rodString);
//}
out.printf("%s%s %s%n", pileup.getPileupString(qualsAsInts), secondBasePileup, rods);
if ( EXTENDED ) {
String probDists = pileup.getProbDistPileup();
@ -108,4 +96,49 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
public Integer treeReduce(Integer lhs, Integer rhs) {
return lhs + rhs;
}
/**
* Should the secondary base be shown under all circumstances?
* @param pileup The ReadBackedPileup at the current locus.
* @return True, if a secondary base pileup should always be shown.
*/
private boolean shouldShowSecondaryBasePileup( ReadBackedPileup pileup ) {
return ( pileup.getSecondaryBasePileup() != null || alwaysShowSecondBase );
}
/**
* Gets second base information for the pileup, if requested.
* @param pileup Pileup from which to extract secondary base info.
* @return String representation of the secondary base.
*/
private String getSecondBasePileup( ReadBackedPileup pileup ) {
String secondBasePileup = pileup.getSecondaryBasePileup();
if( secondBasePileup != null )
return " " + secondBasePileup;
else
return " " + Utils.dupString('N', pileup.getBases().length());
}
/**
* Get a string representation the reference-ordered data.
* @param tracker Container for the reference-ordered data.
* @return String representation of the reference-ordered data.
*/
private String getReferenceOrderedData( RefMetaDataTracker tracker ) {
String rodString = "";
for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {
if ( datum != null && ! (datum instanceof rodDbSNP)) {
rodString += datum.toSimpleString();
}
}
rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null);
if ( dbsnp != null )
rodString += dbsnp.toMediumString();
if ( !rodString.equals("") )
rodString = "[ROD: " + rodString + "]";
return rodString;
}
}

3
packages/GenomeAnalysisTK.xml
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@ -8,6 +8,9 @@
<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
</dependencies>
<resources>
<file>java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
<file>testdata/exampleBAM.bam</file>