@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);
}
