@Test public void testSubtractionOfEmptyChunkLists() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(); GATKBAMFileSpan subtraction = regionOne.minus(regionTwo); Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in subtraction of two empty sets"); }
difference += Math.abs(thisRegion.minus(otherRegion).size());
@Test public void testSubtractionOfStrictSubset() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,1<<16)); GATKBAMFileSpan subtraction = regionOne.minus(regionTwo); Assert.assertEquals(subtraction.getGATKChunks().size(),1,"Incorrect size in strict subset subtraction of region"); Assert.assertEquals(subtraction.getGATKChunks().get(0),new GATKChunk(1<<16,2<<16),"Determined subtraction is incorrect."); }
@Test public void testSubtractionOfPartialOverlap() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,3<<16)); GATKBAMFileSpan subtraction = regionOne.minus(regionTwo); Assert.assertEquals(subtraction.getGATKChunks().size(),1,"Incorrect size in partial subset subtraction of region"); Assert.assertEquals(subtraction.getGATKChunks().get(0),new GATKChunk(0<<16,1<<16),"Determined subtraction is incorrect."); } }
@Test public void testSingleIntervalSubtractedAway() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,1<<16)); GATKBAMFileSpan subtraction = regionOne.minus(regionTwo); Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in complete subtraction of region"); }
@Test public void testMultipleIntervalsSubtractedAway() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) }); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) }); GATKBAMFileSpan subtraction = regionOne.minus(regionTwo); Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in complete subtraction of region"); }