@Test public void exampleFromSamtools(){ // How filters behave: // filterOut(): // Return true if the SAMRecord matches the filter, otherwise false // Example: Keep aligned reads rec.setFlags(0); AlignedFilter f= new AlignedFilter(true); // Set true because we require aligned assertFalse(f.filterOut(rec)); // filterOut() returns false because with flag 0 it's not filtered out. f= new AlignedFilter(false); assertTrue(f.filterOut(rec)); // Exclude if aligned // Keep non aligned reads (flag 4) rec.setFlags(4); f= new AlignedFilter(false); // Keep if non aligned assertFalse(f.filterOut(rec)); // Returns false because read is kept. f= new AlignedFilter(true); // Keep if aligned assertTrue(f.filterOut(rec)); // Exclude read because 4 is non aligned }
isSVAlignment = true; if (UNMAPPED_READS && !unmappedFilter.filterOut(r)) { hasUnmapped[index] = true; hasSV[index] = true;