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Minor cleanup

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1 parent ab1c487 commit dcf2fa361d60ca6810b8c736ce590c3f39ae6f79 @eitanbanks eitanbanks committed Mar 21, 2012
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6 ...ava/src/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java
@@ -1,12 +1,10 @@
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.io.IOException;
import java.util.Iterator;
/**
@@ -24,15 +22,15 @@ public MalformedBAMErrorReformatingIterator(final File source, final CloseableIt
public boolean hasNext() {
try {
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());
}
}
public SAMRecord next() {
try {
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());
}
}

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