@Test(dataProvider = "trimmingData")
public void testTrimTo(
final Map<Haplotype, AssemblyResult> haplotypesAndResultSets, final AssemblyRegion original) {
final AssemblyResultSet subject = new AssemblyResultSet();
for (final Map.Entry<Haplotype, AssemblyResult> entry : haplotypesAndResultSets.entrySet())
subject.add(entry.getKey(), entry.getValue());
subject.setRegionForGenotyping(original);
final GenomeLoc originalLocation = original.getExtendedSpan();
final int length = originalLocation.size();
final GenomeLoc newLocation =
originalLocation.setStop(
originalLocation.setStart(originalLocation, originalLocation.getStart() + length / 2),
originalLocation.getStop() - length / 2);
final AssemblyRegion newRegion = original.trim(newLocation);
final Map<Haplotype, Haplotype> originalHaplotypesByTrimmed =
new HashMap<>(haplotypesAndResultSets.size());
for (final Haplotype h : haplotypesAndResultSets.keySet())
originalHaplotypesByTrimmed.put(h.trim(newRegion.getExtendedSpan()), h);
final AssemblyResultSet trimmed = subject.trimTo(newRegion);
Assert.assertFalse(subject.wasTrimmed());
Assert.assertTrue(trimmed.wasTrimmed());
for (final Haplotype h : trimmed.getHaplotypeList()) {
Assert.assertEquals(h.getGenomeLocation(), newLocation);
Assert.assertEquals(h.getBases().length, newLocation.size());
}
}
public void initialize(final IndexedFastaSequenceFile referenceReader) {
reference =
referenceReader
.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop())
.getBases();
}
/**
* Is this a proper overhang on the right side of the read?
*
* @param readLoc the read's loc
* @param spliceLoc the split's loc
* @return true if it's a right side overhang
*/
protected static boolean isRightOverhang(final GenomeLoc readLoc, final GenomeLoc spliceLoc) {
return readLoc.getStop() >= spliceLoc.getStart()
&& readLoc.getStop() < spliceLoc.getStop()
&& readLoc.getStart() < spliceLoc.getStart();
}