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Merge pull request #365 from broadinstitute/md_kb_improvements 

Fix multiple critical bugs in NA12878 KB
This commit is contained in:
Eric Banks 2013-08-07 06:38:21 -07:00
parent 00f4d767e4 66e1b75118
commit 6d67795916
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java
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@ -29,7 +29,8 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecordIterator;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -154,7 +155,7 @@ public final class LocusIteratorByState extends LocusIterator {
* @param reader a non-null reader
* @param it an iterator from reader that has the reads we want to use to create ReadBackPileups
*/
public LocusIteratorByState(final SAMFileReader reader, final SAMRecordIterator it) {
public LocusIteratorByState(final SAMFileReader reader, final CloseableIterator<SAMRecord> it) {
this(new GATKSAMIterator(it),
new LIBSDownsamplingInfo(false, 0),
true,