@DataProvider(name = "GetOverlapping")
public Object[][] makeGetOverlappingTest() throws Exception {
final GenomeLocParser genomeLocParser =
new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(b37KGReference)));
List<Object[]> tests = new ArrayList<Object[]>();
final GenomeLoc prev1 = genomeLocParser.createGenomeLoc("19", 1, 10);
final GenomeLoc prev2 = genomeLocParser.createGenomeLoc("19", 20, 50);
final GenomeLoc post1 = genomeLocParser.createGenomeLoc("21", 1, 10);
final GenomeLoc post2 = genomeLocParser.createGenomeLoc("21", 20, 50);
final int chr20Length = genomeLocParser.getContigs().getSequence("20").getSequenceLength();
for (final int regionStart : Arrays.asList(1, 10, chr20Length - 10, chr20Length)) {
for (final int regionSize : Arrays.asList(1, 10, 100)) {
final GenomeLoc region =
genomeLocParser.createGenomeLocOnContig("20", regionStart, regionStart + regionSize);
final GenomeLoc spanning =
genomeLocParser.createGenomeLocOnContig("20", regionStart - 10, region.getStop() + 10);
final GenomeLoc before_into =
genomeLocParser.createGenomeLocOnContig("20", regionStart - 10, regionStart + 1);
final GenomeLoc middle =
genomeLocParser.createGenomeLocOnContig("20", regionStart + 1, regionStart + 2);
final GenomeLoc middle_past =
genomeLocParser.createGenomeLocOnContig(
"20", region.getStop() - 1, region.getStop() + 10);
final List<GenomeLoc> potentials = new LinkedList<GenomeLoc>();
potentials.add(region);
if (spanning != null) potentials.add(spanning);
if (before_into != null) potentials.add(before_into);
if (middle != null) potentials.add(middle);
if (middle_past != null) potentials.add(middle_past);
for (final int n : Arrays.asList(1, 2, 3)) {
for (final List<GenomeLoc> regions : Utils.makePermutations(potentials, n, false)) {
tests.add(new Object[] {new GenomeLocSortedSet(genomeLocParser, regions), region});
tests.add(
new Object[] {
new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, prev1)), region
});
tests.add(
new Object[] {
new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, prev1, prev2)),
region
});
tests.add(
new Object[] {
new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, post1)), region
});
tests.add(
new Object[] {
new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, post1, post2)),
region
});
tests.add(
new Object[] {
new GenomeLocSortedSet(genomeLocParser, Utils.append(regions, prev1, post1)),
region
});
tests.add(
new Object[] {
new GenomeLocSortedSet(
genomeLocParser, Utils.append(regions, prev1, prev2, post1, post2)),
region
});
}
}
}
}
return tests.toArray(new Object[][] {});
}
