def test_load_indexed_bam(self):
testFile = self.resourceFile("indexed_bams/sorted.bam")
ac = ADAMContext(self.ss)
reads = ac.loadIndexedBam(testFile,
[ReferenceRegion("chr2", 100, 101),
ReferenceRegion("3", 10, 17)])
self.assertEqual(reads.toDF().count(), 2)
def test_filterByOverlappingRegions(self):
readsPath = self.resourceFile("unsorted.sam")
ac = ADAMContext(self.ss)
reads = ac.loadAlignments(readsPath)
querys = [ReferenceRegion("chr2", 1, 400),
ReferenceRegion("3", 1, 100)]
filtered = reads.filterByOverlappingRegions(querys)
self.assertEqual(filtered.toDF().count(), 2)