diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java index e466aa325..9a468f482 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java +++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java @@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.ReservoirDownsampler; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement; @@ -50,9 +51,6 @@ import java.util.*; /** Iterator that traverses a SAM File, accumulating information on a per-locus basis */ public class LocusIteratorByState extends LocusIterator { -// private static long discarded_bases = 0L; -// private static long observed_bases = 0L; - /** our log, which we want to capture anything from this class */ private static Logger logger = Logger.getLogger(LocusIteratorByState.class); @@ -281,10 +279,9 @@ public class LocusIteratorByState extends LocusIterator { this.genomeLocParser = genomeLocParser; this.samples = new ArrayList(samples); this.readStates = new ReadStateManager(samIterator,readInformation.getDownsamplingMethod()); - } - public LocusIteratorByState(final Iterator samIterator, ReadProperties readInformation, GenomeLocParser genomeLocParser ) { - this(samIterator, readInformation, genomeLocParser, Collections.emptySet()); + if ( this.samples.isEmpty() ) + throw new IllegalArgumentException("samples list must not be empty"); } public Iterator iterator() { diff --git a/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java index 6e9fa0372..dc43b4968 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java @@ -28,10 +28,8 @@ import java.util.*; * testing of the LocusIteratorByState */ public class LocusIteratorByStateUnitTest extends BaseTest { - private final int MAX_READS = 10; private static SAMFileHeader header; private LocusIteratorByState li; - private GenomeLocParser genomeLocParser; @BeforeClass @@ -41,8 +39,11 @@ public class LocusIteratorByStateUnitTest extends BaseTest { } private final LocusIteratorByState makeLTBS(List reads, ReadProperties readAttributes) { + List samples = new ArrayList(); + samples.add(null); + return new LocusIteratorByState(new FakeCloseableIterator(reads.iterator()), - readAttributes,genomeLocParser, new SampleDataSource().getSampleNames()); + readAttributes,genomeLocParser, samples); } @Test