@BeforeClass public void initLiftOver() { liftOver = new LiftOver(CHAIN_FILE); contigMap = liftOver.getContigMap(); }
LiftOver liftOverTool = new LiftOver(new File(ARGS.liftOverChainPath));
@Test(dataProvider = "indelFlipData") public void testFlipIndel(final VariantContext source, final ReferenceSequence reference, final VariantContext result) { final LiftOver liftOver = new LiftOver(CHAIN_FILE); final Interval originalLocus = new Interval(source.getContig(), source.getStart(), source.getEnd()); final Interval target = liftOver.liftOver(originalLocus); if (target != null && !target.isNegativeStrand()) { throw new RuntimeException("not reversed"); } final VariantContext flipped = LiftoverUtils.liftVariant(source, target, reference, false, false); VcfTestUtils.assertEquals(flipped, result); }
@Test(dataProvider = "indelFlipDataWithOriginalAllele") public void testFlipIndelWithOriginalAlleles(final VariantContext source, final ReferenceSequence reference, final VariantContext result) { final LiftOver liftOver = new LiftOver(CHAIN_FILE); final Interval originalLocus = new Interval(source.getContig(), source.getStart(), source.getEnd()); final Interval target = liftOver.liftOver(originalLocus); if (target != null && !target.isNegativeStrand()) { throw new RuntimeException("not reversed"); } final VariantContext flipped = LiftoverUtils.liftVariant(source, target, reference, false, true); VcfTestUtils.assertEquals(flipped, result); }
@Test(dataProvider = "snpWithChangedRef") public void snpWithChangedRef(final VariantContext source, final ReferenceSequence reference, final VariantContext result) { final LiftOver liftOver = new LiftOver(POSITIVE_CHAIN_FILE); final Interval originalLocus = new Interval(source.getContig(), source.getStart(), source.getEnd()); final Interval target = liftOver.liftOver(originalLocus); final VariantContext flipped = LiftoverUtils.swapRefAlt(source, LiftoverUtils.DEFAULT_TAGS_TO_REVERSE, LiftoverUtils.DEFAULT_TAGS_TO_DROP); VcfTestUtils.assertEquals(flipped, result); }
if (REJECT != null) IOUtil.assertFileIsWritable(REJECT); final LiftOver liftOver = new LiftOver(CHAIN); liftOver.setLiftOverMinMatch(MIN_LIFTOVER_PCT);
if (REJECT != null) IOUtil.assertFileIsWritable(REJECT); final LiftOver liftOver = new LiftOver(CHAIN); liftOver.setLiftOverMinMatch(MIN_LIFTOVER_PCT);
final LiftOver liftOver = new LiftOver(CHAIN); liftOver.setShouldLogFailedIntervalsBelowThreshold(LOG_FAILED_INTERVALS);
final LiftOver liftOver = new LiftOver(CHAIN); liftOver.setShouldLogFailedIntervalsBelowThreshold(LOG_FAILED_INTERVALS);
final LiftOver liftOver = new LiftOver(TWO_INTERVAL_CHAIN_FILE);