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Minor cleanup

This commit is contained in:
Eric Banks 2012-03-21 12:14:31 -04:00
parent ab1c48745b
commit dcf2fa361d
1 changed files with 2 additions and 4 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java
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@ -1,12 +1,10 @@
package org.broadinstitute.sting.gatk.iterators; package org.broadinstitute.sting.gatk.iterators;
import net.sf.samtools.SAMFormatException;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File; import java.io.File;
import java.io.IOException;
import java.util.Iterator; import java.util.Iterator;
/** /**
@ -24,7 +22,7 @@ public class MalformedBAMErrorReformatingIterator implements CloseableIterator<S
public boolean hasNext() { public boolean hasNext() {
try { try {
return this.it.hasNext(); return this.it.hasNext();
} catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFileExceptions) sometimes } catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFormatExceptions) sometimes
throw new UserException.MalformedBAM(source, e.getMessage()); throw new UserException.MalformedBAM(source, e.getMessage());
} }
} }
@ -32,7 +30,7 @@ public class MalformedBAMErrorReformatingIterator implements CloseableIterator<S
public SAMRecord next() { public SAMRecord next() {
try { try {
return it.next(); return it.next();
} catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFileExceptions) sometimes } catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFormatExceptions) sometimes
throw new UserException.MalformedBAM(source, e.getMessage()); throw new UserException.MalformedBAM(source, e.getMessage());
} }
} }