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Merged bug fix from Stable into Unstable 

-- Resolved conflict

Conflicts:
	public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
This commit is contained in:
Mark DePristo 2012-02-27 17:13:17 -05:00
parent ca0931c01f 0b29d54937
commit 24356f11b7
8 changed files with 95 additions and 18 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
View File

@ -98,8 +98,8 @@ public final class IntervalBinding<T extends Feature> {
intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(feature));
line = lineReader.readLine();
}
} catch (IOException e) {
throw new UserException("Problem reading the interval file " + featureIntervals.getSource() + "; " + e.getMessage());
} catch (Exception e) {
throw new UserException.MalformedFile(featureIntervals.getSource(), "Problem reading the interval file", e);
}
} else {

34
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
View File

@ -31,6 +31,7 @@ import net.sf.samtools.GATKChunk;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;
@ -193,7 +194,28 @@ public class BAMSchedule implements CloseableIterator<BAMScheduleEntry> {
scheduleFileChannel.close();
}
catch(IOException ex) {
throw new ReviewedStingException("Unable to close schedule file.");
throw makeIOFailureException(true, "Unable to close schedule file.", ex);
}
}
/**
* Convenience routine for creating UserExceptions
* @param wasWriting
* @param message
* @param e
* @return
*/
private final StingException makeIOFailureException(final boolean wasWriting, final String message, final Exception e) {
if ( wasWriting ) {
if ( e == null )
return new UserException.CouldNotCreateOutputFile(scheduleFile, message);
else
return new UserException.CouldNotCreateOutputFile(scheduleFile, message, e);
} else {
if ( e == null )
return new UserException.CouldNotReadInputFile(scheduleFile, message);
else
return new UserException.CouldNotReadInputFile(scheduleFile, message, e);
}
}
@ -297,7 +319,7 @@ public class BAMSchedule implements CloseableIterator<BAMScheduleEntry> {
return scheduleFileChannel.read(buffer);
}
catch(IOException ex) {
throw new ReviewedStingException("Unable to read data from BAM schedule file..",ex);
throw makeIOFailureException(false, "Unable to read data from BAM schedule file.", ex);
}
}
@ -305,10 +327,10 @@ public class BAMSchedule implements CloseableIterator<BAMScheduleEntry> {
try {
scheduleFileChannel.write(buffer);
if(buffer.remaining() > 0)
throw new ReviewedStingException("Unable to write entire buffer to file.");
throw makeIOFailureException(true, "Unable to write entire buffer to file.", null);
}
catch(IOException ex) {
throw new ReviewedStingException("Unable to write data to BAM schedule file.",ex);
throw makeIOFailureException(true, "Unable to write data to BAM schedule file.", ex);
}
}
@ -321,7 +343,7 @@ public class BAMSchedule implements CloseableIterator<BAMScheduleEntry> {
return scheduleFileChannel.position();
}
catch(IOException ex) {
throw new ReviewedStingException("Unable to retrieve position of BAM schedule file.",ex);
throw makeIOFailureException(false, "Unable to retrieve position of BAM schedule file.", ex);
}
}
@ -334,7 +356,7 @@ public class BAMSchedule implements CloseableIterator<BAMScheduleEntry> {
scheduleFileChannel.position(position);
}
catch(IOException ex) {
throw new ReviewedStingException("Unable to position BAM schedule file.",ex);
throw makeIOFailureException(false, "Unable to position BAM schedule file.",ex);
}
}

4
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
View File

@ -579,6 +579,8 @@ public class SAMDataSource {
else {
iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id));
}
iterator = new MalformedBAMErrorReformatingIterator(id.samFile, iterator);
if(shard.getGenomeLocs().size() > 0)
iterator = new IntervalOverlapFilteringIterator(iterator,shard.getGenomeLocs());
iteratorMap.put(readers.getReader(id), iterator);
@ -934,6 +936,8 @@ public class SAMDataSource {
throw new UserException.CouldNotReadInputFile(readerID.samFile, e);
else
throw e;
} catch ( SAMFormatException e ) {
throw new UserException.MalformedBAM(readerID.samFile, e.getMessage());
}
reader.setSAMRecordFactory(factory);
reader.enableFileSource(true);

45
public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java 100644
View File

@ -0,0 +1,45 @@
package org.broadinstitute.sting.gatk.iterators;
import net.sf.samtools.SAMFormatException;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;
import java.util.Iterator;
/**
* Traps BAM formatting errors in underlying iterator and rethrows meaningful GATK UserExceptions
*/
public class MalformedBAMErrorReformatingIterator implements CloseableIterator<SAMRecord> {
File source;
CloseableIterator<SAMRecord> it;
public MalformedBAMErrorReformatingIterator(final File source, final CloseableIterator<SAMRecord> it) {
this.it = it;
this.source = source;
}
public boolean hasNext() {
try {
return this.it.hasNext();
} catch ( SAMFormatException e ) {
throw new UserException.MalformedBAM(source, e.getMessage());
}
}
public SAMRecord next() {
try {
return it.next();
} catch ( SAMFormatException e ) {
throw new UserException.MalformedBAM(source, e.getMessage());
}
}
public void remove() {
throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
}
public void close() { it.close(); }
public Iterator<SAMRecord> iterator() { return this; }
}

16
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
View File

@ -27,13 +27,15 @@ public class NBaseCount extends InfoFieldAnnotation {
int countNBaseSolid = 0;
int countRegularBaseSolid = 0;
for( final Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
for( final PileupElement p : sample.getValue().getBasePileup()) {
if( p.getRead().getReadGroup().getPlatform().toUpperCase().contains("SOLID") ) {
if( BaseUtils.isNBase( p.getBase() ) ) {
countNBaseSolid++;
} else if( BaseUtils.isRegularBase( p.getBase() ) ) {
countRegularBaseSolid++;
for( final AlignmentContext context : stratifiedContexts.values() ) {
if ( context.hasBasePileup() ) { // must be called as getBasePileup may throw error when pileup has no bases
for( final PileupElement p : context.getBasePileup()) {
if( p.getRead().getReadGroup().getPlatform().toUpperCase().contains("SOLID") ) {
if( BaseUtils.isNBase( p.getBase() ) ) {
countNBaseSolid++;
} else if( BaseUtils.isRegularBase( p.getBase() ) ) {
countRegularBaseSolid++;
}
}
}
}

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java
View File

@ -31,8 +31,6 @@ interface VCFLineParser {
* a class that handles the to and from disk for VCF 4 lines
*/
class VCF4Parser implements VCFLineParser {
Set<String> bracketed = new HashSet<String>();
/**
* parse a VCF4 line
* @param valueLine the line

4
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -140,6 +140,10 @@ public class UserException extends ReviewedStingException {
super(String.format("Couldn't write file %s because %s with exception %s", file.getAbsolutePath(), message, e.getMessage()));
}
public CouldNotCreateOutputFile(File file, String message) {
super(String.format("Couldn't write file %s because %s", file.getAbsolutePath(), message));
}
public CouldNotCreateOutputFile(String filename, String message, Exception e) {
super(String.format("Couldn't write file %s because %s with exception %s", filename, message, e.getMessage()));
}

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
View File

@ -29,6 +29,7 @@ import org.broad.tribble.Feature;
import org.broad.tribble.TribbleException;
import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.*;
@ -102,9 +103,10 @@ public class VariantContextBuilder {
* Returns a new builder based on parent -- the new VC will have all fields initialized
* to their corresponding values in parent. This is the best way to create a derived VariantContext
*
* @param parent
* @param parent Cannot be null
*/
public VariantContextBuilder(VariantContext parent) {
if ( parent == null ) throw new ReviewedStingException("BUG: VariantContext parent argument cannot be null in VariantContextBuilder");
this.alleles = parent.alleles;
this.attributes = parent.getAttributes();
this.attributesCanBeModified = false;