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For Ryan: force creation of BAM index when no reads are present in the BAM 

file.  Temporary fix until Picard changes the behavior of indexing.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5351 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-03-02 01:50:42 +00:00
parent 570186fa42
commit dc62685a2f
1 changed files with 40 additions and 5 deletions
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45
java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
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@ -29,8 +29,11 @@ import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator;
import java.io.*;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import net.sf.samtools.util.RuntimeIOException;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.ConstrainedMateFixingSAMFileWriter;
@ -45,6 +48,8 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
private final File file;
private SAMFileWriter writer;
private static Logger logger = Logger.getLogger(SAMFileWriterStorage.class);
public SAMFileWriterStorage( SAMFileWriterStub stub ) {
this(stub,stub.getSAMFile());
}
@ -66,10 +71,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
factory.setCreateIndex(false);
try {
if( stub.getCompressionLevel() != null )
this.writer = factory.makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file, stub.getCompressionLevel() );
else
this.writer = factory.makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file );
this.writer = createBAMWriter(factory,stub.getFileHeader(),stub.isPresorted(),file,stub.getCompressionLevel());
}
catch(RuntimeIOException ex) {
throw new UserException.CouldNotCreateOutputFile(file,"file could not be created",ex);
@ -116,4 +118,37 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
}
}
}
private SAMFileWriter createBAMWriter(final SAMFileWriterFactory factory,
final SAMFileHeader header,
final boolean presorted,
final File outputFile,
final Integer compressionLevel) {
SAMFileWriter writer;
if(compressionLevel != null)
writer = factory.makeBAMWriter(header, presorted, outputFile, compressionLevel);
else
writer = factory.makeBAMWriter(header, presorted, outputFile);
// mhanna - 1 Mar 2011 - temporary hack until Picard generates an index file for empty BAMs --
// - do a pre-initialization of the BAM file.
try {
Method prepareToWriteAlignmentsMethod = writer.getClass().getDeclaredMethod("prepareToWriteAlignments");
if(prepareToWriteAlignmentsMethod != null) {
prepareToWriteAlignmentsMethod.setAccessible(true);
prepareToWriteAlignmentsMethod.invoke(writer);
}
}
catch(NoSuchMethodException ex) {
logger.info("Unable to call prepareToWriteAlignments method; this should be reviewed when Picard is updated.");
}
catch(IllegalAccessException ex) {
logger.info("Unable to access prepareToWriteAlignments method; this should be reviewed when Picard is updated.");
}
catch(InvocationTargetException ex) {
logger.info("Unable to invoke prepareToWriteAlignments method; this should be reviewed when Picard is updated.");
}
return writer;
}
}