public static int getReadCoordinateForReferenceCoordinate(
final int alignmentStart,
final Cigar cigar,
final int refCoord,
final ClippingTail tail,
final boolean allowGoalNotReached) {
Pair<Integer, Boolean> result =
getReadCoordinateForReferenceCoordinate(
alignmentStart, cigar, refCoord, allowGoalNotReached);
int readCoord = result.getFirst();
// Corner case one: clipping the right tail and falls on deletion, move to the next
// read coordinate. It is not a problem for the left tail because the default answer
// from getReadCoordinateForReferenceCoordinate is to give the previous read coordinate.
if (result.getSecond() && tail == ClippingTail.RIGHT_TAIL) readCoord++;
// clipping the left tail and first base is insertion, go to the next read coordinate
// with the same reference coordinate. Advance to the next cigar element, or to the
// end of the read if there is no next element.
Pair<Boolean, CigarElement> firstElementIsInsertion = readStartsWithInsertion(cigar);
if (readCoord == 0 && tail == ClippingTail.LEFT_TAIL && firstElementIsInsertion.getFirst())
readCoord =
Math.min(firstElementIsInsertion.getSecond().getLength(), cigar.getReadLength() - 1);
return readCoord;
}
@Test(dataProvider = "PrefixSuffixData")
public void testPrefixSuffixVertices(
final List<String> strings, int expectedPrefixLen, int expectedSuffixLen) {
final List<SeqVertex> v = new ArrayList<>();
for (final String s : strings) {
v.add(new SeqVertex(s));
}
final String expectedPrefix = strings.get(0).substring(0, expectedPrefixLen);
final String expectedSuffix =
strings.get(0).substring(strings.get(0).length() - expectedSuffixLen);
final Pair<SeqVertex, SeqVertex> result =
SharedVertexSequenceSplitter.commonPrefixAndSuffixOfVertices(v);
Assert.assertEquals(
result.getFirst().getSequenceString(), expectedPrefix, "Failed suffix test");
Assert.assertEquals(
result.getSecond().getSequenceString(), expectedSuffix, "Failed suffix test");
Assert.assertEquals(result.getFirst().isEmpty(), expectedPrefix.isEmpty());
Assert.assertEquals(result.getSecond().isEmpty(), expectedSuffix.isEmpty());
}
/**
* General interval reduce routine called after all of the traversals are done
*
* @param results interval reduce results
*/
public void onTraversalDone(List<Pair<GenomeLoc, ReduceType>> results) {
for (Pair<GenomeLoc, ReduceType> result : results) {
logger.info(String.format("[INTERVAL REDUCE RESULT] at %s ", result.getFirst()));
this.onTraversalDone(result.getSecond());
}
}