@Test(enabled = true) public void testReadWithNsRefAfterDeletion() throws FileNotFoundException { final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); final int readLength = 76; final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength); read.setReadBases(Utils.dupBytes((byte) 'A', readLength)); read.setBaseQualities(Utils.dupBytes((byte) 30, readLength)); read.setCigarString("3M414N1D73M"); final int result = ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead( read, 9393, ReadUtils.ClippingTail.LEFT_TAIL); Assert.assertEquals(result, 3); }