final int sampleReadCount = sampleReads.length;
buffer.ensureCapacity(sampleReadCount);
for (int r = 0; r < sampleReadCount; r++)
if (unclippedReadOverlapsRegion(sampleReads[r], referenceIndex, overlapStart, overlapEnd))
buffer.add(r);
result[s] = buffer.toIntArray();
}
return result;
}
public static boolean unclippedReadOverlapsRegion(final GATKSAMRecord read, final GenomeLoc region) {