diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index a05992cb4..3712e4524 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -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, 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, 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, ReduceRea SortedSet 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, 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, 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, ReduceRea if (!DONT_COMPRESS_READ_NAMES) compressReadName(read); - out.addAlignment(read); + writerToUse.addAlignment(read); } /** diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java b/public/java/src/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java new file mode 100644 index 000000000..6bad58d9f --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java @@ -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 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(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())); + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java b/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java index fa07523f3..83d1c99bf 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java @@ -1,186 +1,188 @@ -/* - * 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.*; -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.*; - -/** - * Created by IntelliJ IDEA. - * User: asivache - * Date: May 31, 2011 - * Time: 3:52:49 PM - * To change this template use File | Settings | File Templates. - */ -public class NWaySAMFileWriter implements SAMFileWriter { - - private Map writerMap = null; - private boolean presorted ; - GenomeAnalysisEngine toolkit; - boolean KEEP_ALL_PG_RECORDS = false; - - public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map in2out, SAMFileHeader.SortOrder order, - boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord, boolean keep_records) { - this.presorted = presorted; - this.toolkit = toolkit; - this.KEEP_ALL_PG_RECORDS = keep_records; - writerMap = new HashMap(); - setupByReader(toolkit,in2out,order, presorted, indexOnTheFly, generateMD5, pRecord); - } - - public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, - boolean presorted, boolean indexOnTheFly , boolean generateMD5, SAMProgramRecord pRecord, boolean keep_records) { - this.presorted = presorted; - this.toolkit = toolkit; - this.KEEP_ALL_PG_RECORDS = keep_records; - writerMap = new HashMap(); - setupByReader(toolkit,ext,order, presorted, indexOnTheFly, generateMD5, pRecord); - } - - public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map in2out, SAMFileHeader.SortOrder order, - boolean presorted, boolean indexOnTheFly, boolean generateMD5) { - this(toolkit, in2out, order, presorted, indexOnTheFly, generateMD5, null,false); - } - - public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, - boolean presorted, boolean indexOnTheFly , boolean generateMD5) { - this(toolkit, ext, order, presorted, indexOnTheFly, generateMD5, null,false); - } - - /** - * Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK engine (those will be retrieved - * from toolkit). The in2out map must contain an entry for each input filename and map it - * onto a unique output file name. - * @param toolkit - * @param in2out - */ - public void setupByReader(GenomeAnalysisEngine toolkit, Map in2out, SAMFileHeader.SortOrder order, - boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord) { - if ( in2out==null ) throw new StingException("input-output bam filename map for n-way-out writing is NULL"); - for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) { - - String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName(); - - String outName; - if ( ! in2out.containsKey(fName) ) - throw new UserException.BadInput("Input-output bam filename map does not contain an entry for the input file "+fName); - outName = in2out.get(fName); - - if ( writerMap.containsKey( rid ) ) - throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered; "+ - "map file likely contains multiple entries for this input file"); - - addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5, pRecord); - } - - } - - /** - * Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK engine (those will be retrieved - * from toolkit). The output file names will be generated automatically by stripping ".sam" or ".bam" off the - * input file name and adding ext instead (e.g. ".cleaned.bam"). - * onto a unique output file name. - * @param toolkit - * @param ext - */ - public void setupByReader(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, - boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord) { - for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) { - - String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName(); - - String outName; - int pos ; - if ( fName.toUpperCase().endsWith(".BAM") ) pos = fName.toUpperCase().lastIndexOf(".BAM"); - else { - if ( fName.toUpperCase().endsWith(".SAM") ) pos = fName.toUpperCase().lastIndexOf(".SAM"); - else throw new UserException.BadInput("Input file name "+fName+" does not end with .sam or .bam"); - } - String prefix = fName.substring(0,pos); - outName = prefix+ext; - - if ( writerMap.containsKey( rid ) ) - throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered"); - addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5, pRecord); - } - - } - - private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted, - boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord programRecord) { - File f = new File(outName); - SAMFileHeader header = toolkit.getSAMFileHeader(id).clone(); - header.setSortOrder(order); - - if ( programRecord != null ) { - // --->> add program record - List oldRecords = header.getProgramRecords(); - List newRecords = new ArrayList(oldRecords.size()+1); - for ( SAMProgramRecord record : oldRecords ) { - if ( !record.getId().startsWith(programRecord.getId()) || KEEP_ALL_PG_RECORDS ) - newRecords.add(record); - } - newRecords.add(programRecord); - header.setProgramRecords(newRecords); - // <-- add program record ends here - } - SAMFileWriterFactory factory = new SAMFileWriterFactory(); - factory.setCreateIndex(indexOnTheFly); - factory.setCreateMd5File(generateMD5); - SAMFileWriter sw = factory.makeSAMOrBAMWriter(header, presorted, f); - writerMap.put(id,sw); - } - - public Collection getWriters() { - return writerMap.values(); - } - - public void addAlignment(SAMRecord samRecord) { - final SAMReaderID id = toolkit.getReaderIDForRead(samRecord); - String rg = samRecord.getStringAttribute("RG"); - if ( rg != null ) { - String rg_orig = toolkit.getReadsDataSource().getOriginalReadGroupId(rg); - samRecord.setAttribute("RG",rg_orig); - } - writerMap.get(id).addAlignment(samRecord); - } - - public SAMFileHeader getFileHeader() { - return toolkit.getSAMFileHeader(); - } - - public void close() { - for ( SAMFileWriter w : writerMap.values() ) w.close(); - } -} +/* + * 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.*; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; +import org.broadinstitute.sting.utils.exceptions.StingException; +import org.broadinstitute.sting.utils.exceptions.UserException; + +import java.io.File; +import java.util.*; + +/** + * Created by IntelliJ IDEA. + * User: asivache + * Date: May 31, 2011 + * Time: 3:52:49 PM + * To change this template use File | Settings | File Templates. + */ +public class NWaySAMFileWriter implements SAMFileWriter { + + private Map writerMap = null; + private boolean presorted ; + GenomeAnalysisEngine toolkit; + boolean KEEP_ALL_PG_RECORDS = false; + + public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map in2out, SAMFileHeader.SortOrder order, + boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord, boolean keep_records) { + this.presorted = presorted; + this.toolkit = toolkit; + this.KEEP_ALL_PG_RECORDS = keep_records; + writerMap = new HashMap(); + setupByReader(toolkit,in2out,order, presorted, indexOnTheFly, generateMD5, pRecord); + } + + public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, + boolean presorted, boolean indexOnTheFly , boolean generateMD5, SAMProgramRecord pRecord, boolean keep_records) { + this.presorted = presorted; + this.toolkit = toolkit; + this.KEEP_ALL_PG_RECORDS = keep_records; + writerMap = new HashMap(); + setupByReader(toolkit,ext,order, presorted, indexOnTheFly, generateMD5, pRecord); + } + + public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map in2out, SAMFileHeader.SortOrder order, + boolean presorted, boolean indexOnTheFly, boolean generateMD5) { + this(toolkit, in2out, order, presorted, indexOnTheFly, generateMD5, null,false); + } + + public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, + boolean presorted, boolean indexOnTheFly , boolean generateMD5) { + this(toolkit, ext, order, presorted, indexOnTheFly, generateMD5, null,false); + } + + /** + * Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK engine (those will be retrieved + * from toolkit). The in2out map must contain an entry for each input filename and map it + * onto a unique output file name. + * @param toolkit + * @param in2out + */ + public void setupByReader(GenomeAnalysisEngine toolkit, Map in2out, SAMFileHeader.SortOrder order, + boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord) { + if ( in2out==null ) throw new StingException("input-output bam filename map for n-way-out writing is NULL"); + for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) { + + String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName(); + + String outName; + if ( ! in2out.containsKey(fName) ) + throw new UserException.BadInput("Input-output bam filename map does not contain an entry for the input file "+fName); + outName = in2out.get(fName); + + if ( writerMap.containsKey( rid ) ) + throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered; "+ + "map file likely contains multiple entries for this input file"); + + addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5, pRecord); + } + + } + + /** + * Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK engine (those will be retrieved + * from toolkit). The output file names will be generated automatically by stripping ".sam" or ".bam" off the + * input file name and adding ext instead (e.g. ".cleaned.bam"). + * onto a unique output file name. + * @param toolkit + * @param ext + */ + public void setupByReader(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, + boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord) { + for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) { + + String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName(); + + String outName; + int pos ; + if ( fName.toUpperCase().endsWith(".BAM") ) pos = fName.toUpperCase().lastIndexOf(".BAM"); + else { + if ( fName.toUpperCase().endsWith(".SAM") ) pos = fName.toUpperCase().lastIndexOf(".SAM"); + else throw new UserException.BadInput("Input file name "+fName+" does not end with .sam or .bam"); + } + String prefix = fName.substring(0,pos); + outName = prefix+ext; + + if ( writerMap.containsKey( rid ) ) + throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered"); + addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5, pRecord); + } + + } + + private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted, + boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord programRecord) { + File f = new File(outName); + SAMFileHeader header = toolkit.getSAMFileHeader(id).clone(); + header.setSortOrder(order); + + if ( programRecord != null ) { + // --->> add program record + List oldRecords = header.getProgramRecords(); + List newRecords = new ArrayList(oldRecords.size()+1); + for ( SAMProgramRecord record : oldRecords ) { + if ( !record.getId().startsWith(programRecord.getId()) || KEEP_ALL_PG_RECORDS ) + newRecords.add(record); + } + newRecords.add(programRecord); + header.setProgramRecords(newRecords); + // <-- add program record ends here + } + SAMFileWriterFactory factory = new SAMFileWriterFactory(); + factory.setCreateIndex(indexOnTheFly); + factory.setCreateMd5File(generateMD5); + SAMFileWriter sw = factory.makeSAMOrBAMWriter(header, presorted, f); + writerMap.put(id,sw); + } + + public Collection getWriters() { + return writerMap.values(); + } + + public void addAlignment(SAMRecord samRecord) { + final SAMReaderID id = toolkit.getReaderIDForRead(samRecord); + String rg = samRecord.getStringAttribute("RG"); + if ( rg != null ) { + String rg_orig = toolkit.getReadsDataSource().getOriginalReadGroupId(rg); + samRecord.setAttribute("RG",rg_orig); + } + addAlignment(samRecord, id); + } + + public void addAlignment(SAMRecord samRecord, SAMReaderID readerID) { + writerMap.get(readerID).addAlignment(samRecord); + } + + public SAMFileHeader getFileHeader() { + return toolkit.getSAMFileHeader(); + } + + public void close() { + for ( SAMFileWriter w : writerMap.values() ) w.close(); + } +}