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Implementation of BySampleSAMFileWriter 

ReduceReads now works with the n-way-out capability, splitting by sample.
DEV-27 #resolve #time 3m
This commit is contained in:
Mauricio Carneiro 2012-11-13 01:18:37 -05:00
parent 1f23a82aa4
commit 95a4ba57bf
3 changed files with 290 additions and 191 deletions
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37
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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@ -25,6 +25,9 @@
package org.broadinstitute.sting.gatk.walkers.compression.reducereads;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMProgramRecord;
import net.sf.samtools.util.SequenceUtil;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
@ -45,6 +48,7 @@ import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.BySampleSAMFileWriter;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -86,7 +90,8 @@ import java.util.*;
public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceReadsStash> {
@Output
private StingSAMFileWriter out;
private StingSAMFileWriter out = null;
private SAMFileWriter writerToUse = null;
/**
* The number of bases to keep around mismatches (potential variation)
@ -196,6 +201,10 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
@Argument(fullName = "contigs", shortName = "ctg", doc = "", required = false)
private int nContigs = 2;
@Hidden
@Argument(fullName = "nwayout", shortName = "nw", doc = "", required = false)
private boolean nwayout = false;
@Hidden
@Argument(fullName = "", shortName = "dl", doc = "", required = false)
private int debugLevel = 0;
@ -227,6 +236,7 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
SortedSet<GenomeLoc> intervalList;
private static final String PROGRAM_RECORD_NAME = "GATK ReduceReads"; // The name that will go in the @PG tag
private static final String PROGRAM_FILENAME_EXTENSION = ".reduced.bam";
/**
* Basic generic initialization of the readNameHash and the intervalList. Output initialization
@ -242,10 +252,24 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
if (toolkit.getIntervals() != null)
intervalList.addAll(toolkit.getIntervals());
if (!NO_PG_TAG)
Utils.setupWriter(out, toolkit, false, true, this, PROGRAM_RECORD_NAME);
else
// todo -- rework the whole NO_PG_TAG thing
final boolean preSorted = true;
final boolean indexOnTheFly = true;
final boolean generateMD5 = true;
final boolean keep_records = true;
final SAMFileHeader.SortOrder sortOrder = SAMFileHeader.SortOrder.coordinate;
if (nwayout) {
SAMProgramRecord programRecord = NO_PG_TAG ? null : Utils.createProgramRecord(toolkit, this, PROGRAM_RECORD_NAME);
writerToUse = new BySampleSAMFileWriter(toolkit, PROGRAM_FILENAME_EXTENSION, sortOrder, preSorted, indexOnTheFly, NO_PG_TAG, programRecord, true);
}
else {
writerToUse = out;
out.setPresorted(false);
if (!NO_PG_TAG) {
Utils.setupWriter(out, toolkit, !preSorted, keep_records, this, PROGRAM_RECORD_NAME);
}
}
}
/**
@ -386,6 +410,9 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
// output any remaining reads in the compressor
for (GATKSAMRecord read : stash.close())
outputRead(read);
if (nwayout)
writerToUse.close();
}
/**
@ -554,7 +581,7 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
if (!DONT_COMPRESS_READ_NAMES)
compressReadName(read);
out.addAlignment(read);
writerToUse.addAlignment(read);
}
/**

70
public/java/src/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java 100644
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@ -0,0 +1,70 @@
/*
* Copyright (c) 2010 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.utils.sam;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMProgramRecord;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.HashMap;
import java.util.Map;
/**
* Created by IntelliJ IDEA.
* User: carneiro
* Date: Nov 13
*/
public class BySampleSAMFileWriter extends NWaySAMFileWriter{
private final Map<String, SAMReaderID> sampleToWriterMap;
public BySampleSAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord, boolean keep_records) {
super(toolkit, ext, order, presorted, indexOnTheFly, generateMD5, pRecord, keep_records);
sampleToWriterMap = new HashMap<String, SAMReaderID>(toolkit.getSAMFileHeader().getReadGroups().size() * 2);
for (SAMReaderID readerID : toolkit.getReadsDataSource().getReaderIDs()) {
for (SAMReadGroupRecord rg : toolkit.getReadsDataSource().getHeader(readerID).getReadGroups()) {
String sample = rg.getSample();
if (sampleToWriterMap.containsKey(sample) && sampleToWriterMap.get(sample) != readerID) {
throw new ReviewedStingException("The same sample appears in multiple files, this input cannot be multiplexed using the BySampleSAMFileWriter, try NWaySAMFileWriter instead.");
}
else {
sampleToWriterMap.put(sample, readerID);
}
}
}
}
@Override
public void addAlignment(SAMRecord samRecord) {
super.addAlignment(samRecord, sampleToWriterMap.get(samRecord.getReadGroup().getSample()));
}
}

8
public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
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@ -28,10 +28,8 @@ package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.io.File;
import java.util.*;
@ -173,7 +171,11 @@ public class NWaySAMFileWriter implements SAMFileWriter {
String rg_orig = toolkit.getReadsDataSource().getOriginalReadGroupId(rg);
samRecord.setAttribute("RG",rg_orig);
}
writerMap.get(id).addAlignment(samRecord);
addAlignment(samRecord, id);
}
public void addAlignment(SAMRecord samRecord, SAMReaderID readerID) {
writerMap.get(readerID).addAlignment(samRecord);
}
public SAMFileHeader getFileHeader() {