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Added "simplify reads" option to PrintReads.

This commit is contained in:
Mauricio Carneiro 2012-04-12 14:09:18 -04:00
parent f0c81b59b0
commit 46a212d8e9
2 changed files with 15 additions and 8 deletions
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20
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
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@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@ -91,7 +90,7 @@ import java.util.TreeSet;
*/
@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
@Requires({DataSource.READS, DataSource.REFERENCE})
public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
public class PrintReadsWalker extends ReadWalker<GATKSAMRecord, SAMFileWriter> {
@Output(doc="Write output to this BAM filename instead of STDOUT")
SAMFileWriter out;
@ -129,6 +128,13 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
@Argument(fullName="sample_name", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false)
public Set<String> sampleNames = new TreeSet<String>();
/**
* Erase all extra attributes in the read but keep the read group information
*/
@Argument(fullName="simplify", shortName="s", doc="Simplify all reads.", required=false)
public boolean simplifyReads = false;
private TreeSet<String> samplesToChoose = new TreeSet<String>();
private boolean SAMPLES_SPECIFIED = false;
@ -162,7 +168,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
* The reads filter function.
*
* @param ref the reference bases that correspond to our read, if a reference was provided
* @param read the read itself, as a SAMRecord
* @param read the read itself, as a GATKSAMRecord
* @return true if the read passes the filter, false if it doesn't
*/
public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
@ -208,11 +214,11 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
* The reads map function.
*
* @param ref the reference bases that correspond to our read, if a reference was provided
* @param read the read itself, as a SAMRecord
* @param read the read itself, as a GATKSAMRecord
* @return the read itself
*/
public SAMRecord map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
return read;
public GATKSAMRecord map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
return simplifyReads ? read.simplify() : read;
}
/**
@ -232,7 +238,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
* @param output the output source
* @return the SAMFileWriter, so that the next reduce can emit to the same source
*/
public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
public SAMFileWriter reduce( GATKSAMRecord read, SAMFileWriter output ) {
output.addAlignment(read);
return output;
}

3
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -335,10 +335,11 @@ public class GATKSAMRecord extends BAMRecord {
/**
* Clears all attributes except ReadGroup of the read.
*/
public void simplify () {
public GATKSAMRecord simplify () {
GATKSAMReadGroupRecord rg = getReadGroup();
this.clearAttributes();
setReadGroup(rg);
return this;
}
/**