Fixed file handle leak in VariantCallIterator.

Added defensive GC to SAMEvidenceSource to reduce likelihood of running out of file handles due to unfinialised htsjdk memory mapped buffers

pom.xml

@@ -4,7 +4,7 @@
 	<groupId>au.edu.wehi</groupId>
 	<artifactId>gridss</artifactId>
 	<packaging>jar</packaging>
-	<version>1.3.3</version>
+	<version>1.3.4</version>
 	<name>gridss</name>
 	<url>https://github.com/PapenfussLab/gridss</url>
 	<properties>

src/main/java/au/edu/wehi/idsv/SAMEvidenceSource.java

@@ -244,14 +244,37 @@ public void ensureExtracted() throws IOException {
 	public CloseableIterator<DirectedEvidence> iterator(final QueryInterval interval) {
 		SamReader reader = getReader();
 		// expand query bounds as the alignment for a discordant read pair could fall before or after the breakend interval we are extracting
-		SAMRecordIterator it = reader.queryOverlapping(new QueryInterval[] {
-			new QueryInterval(interval.referenceIndex, interval.start - getMaxConcordantFragmentSize() - 1, interval.end + getMaxConcordantFragmentSize() + 1)});
+		SAMRecordIterator it = tryOpenReader(reader, new QueryInterval(interval.referenceIndex, interval.start - getMaxConcordantFragmentSize() - 1, interval.end + getMaxConcordantFragmentSize() + 1));
 		Iterator<DirectedEvidence> eit = asEvidence(it);
 		final BreakendSummary bsf = new BreakendSummary(interval.referenceIndex, BreakendDirection.Forward, interval.start, interval.start, interval.end);
 		final BreakendSummary bsb = new BreakendSummary(interval.referenceIndex, BreakendDirection.Backward, interval.start, interval.start, interval.end);
 		eit = Iterators.filter(eit, e -> bsf.overlaps(e.getBreakendSummary()) || bsb.overlaps(e.getBreakendSummary()));
 		return new AutoClosingIterator<>(eit, reader, it);
 	}
+	/**
+	 * Attempts to open a new iterator.
+	 * 
+	 * As htsjdk performing memory mapping internally, many open/close cycles can results in an exhaustion
+	 * of file handles. 
+	 * 
+	 * @param reader
+	 * @param interval
+	 * @return
+	 */
+	private SAMRecordIterator tryOpenReader(SamReader reader, QueryInterval interval) {
+		SAMRecordIterator it = null;
+		try {
+			it = reader.queryOverlapping(new QueryInterval[] { interval });
+		} catch (Exception e) {
+			log.debug("Attempting to recover from query failure: ", e);
+			System.gc();
+			System.runFinalization();
+			System.gc();
+			it = reader.queryOverlapping(new QueryInterval[] { interval });
+			log.debug("Recovery successful");
+		}
+		return it;
+	}
 	public CloseableIterator<DirectedEvidence> iterator() {
 		SamReader reader = getReader();
 		SAMRecordIterator it = reader.iterator();

src/main/java/au/edu/wehi/idsv/VariantCallIterator.java

@@ -29,6 +29,7 @@ public class VariantCallIterator implements CloseableIterator<VariantContextDire
 	private final Supplier<Iterator<DirectedEvidence>> iteratorGenerator;
 	private final QueryInterval filterInterval;
 	private Iterator<VariantContextDirectedBreakpoint> currentIterator;
+	private Iterator<DirectedEvidence> currentUnderlyingIterator;
 	private int currentDirectionOrdinal;
 	public VariantCallIterator(ProcessingContext processContext, Iterable<DirectedEvidence> evidence) throws InterruptedException {
 		this.processContext = processContext;
@@ -59,10 +60,12 @@ public VariantCallIterator(AggregateEvidenceSource source, QueryInterval interva
 	private void reinitialiseIterator() {
 		assert(currentIterator == null || !currentIterator.hasNext());
 		CloserUtil.close(currentIterator);
-		if (currentDirectionOrdinal >= DIRECTION_ORDER.size()) return; 
+		CloserUtil.close(currentUnderlyingIterator);
+		if (currentDirectionOrdinal >= DIRECTION_ORDER.size()) return;
+		currentUnderlyingIterator = iteratorGenerator.get();
 		currentIterator = new MaximalEvidenceCliqueIterator(
 				processContext,
-				iteratorGenerator.get(),
+				currentUnderlyingIterator,
 				DIRECTION_ORDER.get(currentDirectionOrdinal).getLeft(),
 				DIRECTION_ORDER.get(currentDirectionOrdinal).getRight(),
 				idGenerator);
@@ -92,6 +95,7 @@ public VariantContextDirectedBreakpoint next() {
 	@Override
 	public void close() {
 		CloserUtil.close(currentIterator);
+		CloserUtil.close(currentUnderlyingIterator);
 	}
 }