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Merged bug fix from Stable into Unstable

This commit is contained in:
Mark DePristo 2012-04-10 09:42:09 -04:00
parent cd9bf1bfc3 6885e2d065
commit b43d21056b
2 changed files with 17 additions and 19 deletions
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31
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
View File

@ -51,11 +51,10 @@ import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory; import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory;
import java.io.File; import java.io.File;
import java.io.FileNotFoundException;
import java.lang.reflect.InvocationTargetException; import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method; import java.lang.reflect.Method;
import java.util.*; import java.util.*;
import java.util.concurrent.*; import java.util.concurrent.Callable;
/** /**
* User: aaron * User: aaron
@ -466,7 +465,6 @@ public class SAMDataSource {
/** /**
* Fill the given buffering shard with reads. * Fill the given buffering shard with reads.
* @param shard Shard to fill. * @param shard Shard to fill.
* @return true if at the end of the stream. False otherwise.
*/ */
public void fillShard(Shard shard) { public void fillShard(Shard shard) {
if(!shard.buffersReads()) if(!shard.buffersReads())
@ -561,15 +559,19 @@ public class SAMDataSource {
if(shard.getFileSpans().get(id) == null) if(shard.getFileSpans().get(id) == null)
throw new ReviewedStingException("SAMDataSource: received null location for reader " + id + ", but null locations are no longer supported."); throw new ReviewedStingException("SAMDataSource: received null location for reader " + id + ", but null locations are no longer supported.");
if(threadAllocation.getNumIOThreads() > 0) { try {
BlockInputStream inputStream = readers.getInputStream(id); if(threadAllocation.getNumIOThreads() > 0) {
inputStream.submitAccessPlan(new BAMAccessPlan(id, inputStream, (GATKBAMFileSpan) shard.getFileSpans().get(id))); BlockInputStream inputStream = readers.getInputStream(id);
BAMRecordCodec codec = new BAMRecordCodec(getHeader(id),factory); inputStream.submitAccessPlan(new BAMAccessPlan(id, inputStream, (GATKBAMFileSpan) shard.getFileSpans().get(id)));
codec.setInputStream(inputStream); BAMRecordCodec codec = new BAMRecordCodec(getHeader(id),factory);
iterator = new BAMCodecIterator(inputStream,readers.getReader(id),codec); codec.setInputStream(inputStream);
} iterator = new BAMCodecIterator(inputStream,readers.getReader(id),codec);
else { }
iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id)); else {
iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id));
}
} catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFormatExceptions) sometimes
throw new UserException.MalformedBAM(id.samFile, e.getMessage());
} }
iterator = new MalformedBAMErrorReformatingIterator(id.samFile, iterator); iterator = new MalformedBAMErrorReformatingIterator(id.samFile, iterator);
@ -924,10 +926,7 @@ public class SAMDataSource {
blockInputStream = new BlockInputStream(dispatcher,readerID,false); blockInputStream = new BlockInputStream(dispatcher,readerID,false);
reader = new SAMFileReader(readerID.samFile,indexFile,false); reader = new SAMFileReader(readerID.samFile,indexFile,false);
} catch ( RuntimeIOException e ) { } catch ( RuntimeIOException e ) {
if ( e.getCause() != null && e.getCause() instanceof FileNotFoundException ) throw new UserException.CouldNotReadInputFile(readerID.samFile, e);
throw new UserException.CouldNotReadInputFile(readerID.samFile, e);
else
throw e;
} catch ( SAMFormatException e ) { } catch ( SAMFormatException e ) {
throw new UserException.MalformedBAM(readerID.samFile, e.getMessage()); throw new UserException.MalformedBAM(readerID.samFile, e.getMessage());
} }

5
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
View File

@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.walkers.variantutils; package org.broadinstitute.sting.gatk.walkers.variantutils;
import net.sf.picard.PicardException;
import net.sf.picard.liftover.LiftOver; import net.sf.picard.liftover.LiftOver;
import net.sf.picard.util.Interval; import net.sf.picard.util.Interval;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
@ -73,7 +72,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
public void initialize() { public void initialize() {
try { try {
liftOver = new LiftOver(CHAIN); liftOver = new LiftOver(CHAIN);
} catch (PicardException e) { } catch (RuntimeException e) {
throw new UserException.BadInput("there is a problem with the chain file you are using: " + e.getMessage()); throw new UserException.BadInput("there is a problem with the chain file you are using: " + e.getMessage());
} }
@ -82,7 +81,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
try { try {
final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader(); final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader();
liftOver.validateToSequences(toHeader.getSequenceDictionary()); liftOver.validateToSequences(toHeader.getSequenceDictionary());
} catch (PicardException e) { } catch (RuntimeException e) {
throw new UserException.BadInput("the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference"); throw new UserException.BadInput("the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference");
} }