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Merged bug fix from Stable into Unstable

This commit is contained in:
Matt Hanna 2011-10-05 20:37:43 -04:00
parent b945e97de1 55b9f06527
commit 180c8f286f
2 changed files with 18 additions and 13 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -248,6 +248,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Argument(fullName="nWayOut", shortName="nWayOut", required=false, doc="Generate one output file for each input (-I) bam file") @Argument(fullName="nWayOut", shortName="nWayOut", required=false, doc="Generate one output file for each input (-I) bam file")
protected String N_WAY_OUT = null; protected String N_WAY_OUT = null;
@Hidden
@Argument(fullName="generate_nWayOut_md5s",doc="Generate md5sums for BAMs")
protected boolean generateMD5s = false;
// DEBUGGING OPTIONS FOLLOW // DEBUGGING OPTIONS FOLLOW
@ -401,9 +404,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// if ( args.containsKey("disable_bam_indexing") ) { System.out.println("NO INDEXING!!"); System.exit(1); createIndex = false; } // if ( args.containsKey("disable_bam_indexing") ) { System.out.println("NO INDEXING!!"); System.exit(1); createIndex = false; }
if ( N_WAY_OUT.toUpperCase().endsWith(".MAP") ) { if ( N_WAY_OUT.toUpperCase().endsWith(".MAP") ) {
writerToUse = new NWaySAMFileWriter(getToolkit(),loadFileNameMap(N_WAY_OUT),SAMFileHeader.SortOrder.coordinate,true, createIndex); writerToUse = new NWaySAMFileWriter(getToolkit(),loadFileNameMap(N_WAY_OUT),SAMFileHeader.SortOrder.coordinate,true, createIndex, generateMD5s);
} else { } else {
writerToUse = new NWaySAMFileWriter(getToolkit(),N_WAY_OUT,SAMFileHeader.SortOrder.coordinate,true, createIndex); writerToUse = new NWaySAMFileWriter(getToolkit(),N_WAY_OUT,SAMFileHeader.SortOrder.coordinate,true, createIndex, generateMD5s);
} }
} else { } else {

24
public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
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@ -51,18 +51,18 @@ public class NWaySAMFileWriter implements SAMFileWriter {
private boolean presorted ; private boolean presorted ;
GenomeAnalysisEngine toolkit; GenomeAnalysisEngine toolkit;
public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) { public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly, boolean generateMD5) {
this.presorted = presorted; this.presorted = presorted;
this.toolkit = toolkit; this.toolkit = toolkit;
writerMap = new HashMap<SAMReaderID,SAMFileWriter>(); writerMap = new HashMap<SAMReaderID,SAMFileWriter>();
setupByReader(toolkit,in2out,order, presorted, indexOnTheFly); setupByReader(toolkit,in2out,order, presorted, indexOnTheFly, generateMD5);
} }
public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly ) { public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly , boolean generateMD5) {
this.presorted = presorted; this.presorted = presorted;
this.toolkit = toolkit; this.toolkit = toolkit;
writerMap = new HashMap<SAMReaderID,SAMFileWriter>(); writerMap = new HashMap<SAMReaderID,SAMFileWriter>();
setupByReader(toolkit,ext,order, presorted, indexOnTheFly); setupByReader(toolkit,ext,order, presorted, indexOnTheFly, generateMD5);
} }
@ -73,8 +73,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
* @param toolkit * @param toolkit
* @param in2out * @param in2out
*/ */
public void setupByReader(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) { public void setupByReader(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly, boolean generateMD5) {
if ( in2out==null ) throw new StingException("input-output bam filename map for n-way-out writing is NULL"); if ( in2out==null ) throw new StingException("input-output bam filename map for n-way-out writing is NULL");
for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) { for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
@ -88,7 +87,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
if ( writerMap.containsKey( rid ) ) if ( writerMap.containsKey( rid ) )
throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered"); throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
addWriter(rid,outName, order, presorted, indexOnTheFly); addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5);
} }
} }
@ -101,7 +100,7 @@ public class NWaySAMFileWriter implements SAMFileWriter {
* @param toolkit * @param toolkit
* @param ext * @param ext
*/ */
public void setupByReader(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) { public void setupByReader(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly, boolean generateMD5) {
for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) { for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName(); String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();
@ -119,16 +118,19 @@ public class NWaySAMFileWriter implements SAMFileWriter {
if ( writerMap.containsKey( rid ) ) if ( writerMap.containsKey( rid ) )
throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered"); throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
addWriter(rid,outName, order, presorted, indexOnTheFly); addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5);
} }
} }
private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly) { private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted, boolean indexOnTheFly, boolean generateMD5) {
File f = new File(outName); File f = new File(outName);
SAMFileHeader header = toolkit.getSAMFileHeader(id).clone(); SAMFileHeader header = toolkit.getSAMFileHeader(id).clone();
header.setSortOrder(order); header.setSortOrder(order);
SAMFileWriter sw = new SAMFileWriterFactory().setCreateIndex(indexOnTheFly).makeSAMOrBAMWriter(header, presorted, f); SAMFileWriterFactory factory = new SAMFileWriterFactory();
factory.setCreateIndex(indexOnTheFly);
factory.setCreateMd5File(generateMD5);
SAMFileWriter sw = factory.makeSAMOrBAMWriter(header, presorted, f);
writerMap.put(id,sw); writerMap.put(id,sw);
} }