@Test(dataProvider = "LIBSTest") public void testLIBS(LIBSTest params) { final int locus = 44367788; SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, locus, params.readLength); read.setReadBases(Utils.dupBytes((byte) 'A', params.readLength)); read.setBaseQualities(Utils.dupBytes((byte) '@', params.readLength)); read.setCigarString(params.cigar); // create the iterator by state with the fake reads and fake records li = makeLTBS(Arrays.asList(read), createTestReadProperties()); final LIBS_position tester = new LIBS_position(read); while (li.hasNext()) { AlignmentContext alignmentContext = li.next(); ReadBackedPileup p = alignmentContext.getBasePileup(); Assert.assertTrue(p.getNumberOfElements() == 1); PileupElement pe = p.iterator().next(); tester.stepForwardOnGenome(); Assert.assertEquals(pe.isBeforeDeletedBase(), tester.isBeforeDeletedBase); Assert.assertEquals(pe.isBeforeDeletionStart(), tester.isBeforeDeletionStart); Assert.assertEquals(pe.isAfterDeletedBase(), tester.isAfterDeletedBase); Assert.assertEquals(pe.isAfterDeletionEnd(), tester.isAfterDeletionEnd); Assert.assertEquals(pe.isBeforeInsertion(), tester.isBeforeInsertion); Assert.assertEquals(pe.isAfterInsertion(), tester.isAfterInsertion); Assert.assertEquals(pe.isNextToSoftClip(), tester.isNextToSoftClip); Assert.assertEquals(pe.getOffset(), tester.getCurrentReadOffset()); } }