Updated async runner to latest patch

PapenfussLab · Mar 8, 2019 · 9ea5ecf · 9ea5ecf
1 parent 8f2109e
commit 9ea5ecf
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/src/main/java/htsjdk/samtools/util/AsyncReadTaskRunner.java b/src/main/java/htsjdk/samtools/util/AsyncReadTaskRunner.java
@@ -199,11 +199,11 @@ private Deque<RecordOrException<U>> readNextBatch() {
                 Tuple<U, Long> ra;
                 try {
                     ra = performReadAhead(mBatchBufferBudget - bufferConsumed);
-                    if (ra.a == null) {
+                    if (ra == null || ra.a == null) {
                         eosReached = true;
                     }
-                    batch.addLast(new RecordOrException(ra.a));
-                    if (ra.b == 0 || ra.b == null) {
+                    batch.addLast(new RecordOrException(ra == null ? null : ra.a));
+                    if (ra == null || ra.b == 0 || ra.b == null) {
                         // performReadAhead() keeps returning 0 to us, we'll never exit
                         break; // safety exit to ensure we are guaranteed to finish the batch
                     }