private GenomeLoc createIntervalAfter(GenomeLoc interval) {
int contigLimit =
getToolkit()
.getSAMFileHeader()
.getSequenceDictionary()
.getSequence(interval.getContigIndex())
.getSequenceLength();
int start = Math.min(interval.getStop() + 1, contigLimit);
int stop = Math.min(interval.getStop() + expandInterval, contigLimit);
return parser.createGenomeLoc(interval.getContig(), interval.getContigIndex(), start, stop);
}
@Test
public void deleteSuperRegion() {
GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 10, 20);
GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 70, 100);
mSortedSet.add(g);
mSortedSet.addRegion(e);
assertTrue(mSortedSet.size() == 2);
// now delete a region
GenomeLoc d = genomeLocParser.createGenomeLoc(contigOneName, 15, 75);
mSortedSet = mSortedSet.subtractRegions(new GenomeLocSortedSet(genomeLocParser, d));
Iterator<GenomeLoc> iter = mSortedSet.iterator();
GenomeLoc loc = iter.next();
assertTrue(loc.getStart() == 10);
assertTrue(loc.getStop() == 14);
assertTrue(loc.getContigIndex() == 1);
loc = iter.next();
assertTrue(loc.getStart() == 76);
assertTrue(loc.getStop() == 100);
assertTrue(loc.getContigIndex() == 1);
}
/**
* Adds a GenomeLoc to the collection, merging it if it overlaps another region. If it's not
* overlapping then we add it in sorted order.
*
* @param e the GenomeLoc to add to the collection
* @return true, if the GenomeLoc could be added to the collection
*/
public boolean addRegion(GenomeLoc e) {
if (e == null) {
return false;
}
// have we added it to the collection?
boolean haveAdded = false;
/**
* check if the specified element overlaps any current locations, if so we should merge the two.
*/
for (GenomeLoc g : mArray) {
if (g.contiguousP(e)) {
GenomeLoc c = g.merge(e);
mArray.set(mArray.indexOf(g), c);
haveAdded = true;
} else if ((g.getContigIndex() == e.getContigIndex())
&& (e.getStart() < g.getStart())
&& !haveAdded) {
mArray.add(mArray.indexOf(g), e);
return true;
} else if (haveAdded
&& ((e.getContigIndex() > e.getContigIndex())
|| (g.getContigIndex() == e.getContigIndex() && e.getStart() > g.getStart()))) {
return true;
}
}
/**
* we're at the end and we haven't found locations that should fall after it, so we'll put it at
* the end
*/
if (!haveAdded) {
mArray.add(e);
}
return true;
}
@Test
public void fromSequenceDictionary() {
mSortedSet =
GenomeLocSortedSet.createSetFromSequenceDictionary(this.header.getSequenceDictionary());
// we should have sequence
assertTrue(mSortedSet.size() == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);
int seqNumber = 0;
for (GenomeLoc loc : mSortedSet) {
assertTrue(loc.getStart() == 1);
assertTrue(loc.getStop() == GenomeLocSortedSetUnitTest.CHROMOSOME_SIZE);
assertTrue(loc.getContigIndex() == seqNumber);
++seqNumber;
}
assertTrue(seqNumber == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);
}
@Test
public void mergingOverlappingAbove() {
GenomeLoc e = genomeLocParser.createGenomeLoc(contigOneName, 0, 50);
GenomeLoc g = genomeLocParser.createGenomeLoc(contigOneName, 49, 100);
assertTrue(mSortedSet.size() == 0);
mSortedSet.add(g);
assertTrue(mSortedSet.size() == 1);
mSortedSet.addRegion(e);
assertTrue(mSortedSet.size() == 1);
Iterator<GenomeLoc> iter = mSortedSet.iterator();
GenomeLoc loc = iter.next();
assertEquals(loc.getStart(), 0);
assertEquals(loc.getStop(), 100);
assertEquals(loc.getContigIndex(), 1);
}
private GenomeLoc createIntervalBefore(GenomeLoc interval) {
int start = Math.max(interval.getStart() - expandInterval, 0);
int stop = Math.max(interval.getStart() - 1, 0);
return parser.createGenomeLoc(interval.getContig(), interval.getContigIndex(), start, stop);
}