public String toString() { StringBuilder builder = new StringBuilder(); for(GATKChunk chunk: getGATKChunks()) builder.append(String.format("%s;",chunk)); return builder.toString(); }
BAMAccessPlan(final SAMReaderID reader, final BlockInputStream inputStream, GATKBAMFileSpan fileSpan) { this.reader = reader; this.inputStream = inputStream; this.positions = fileSpan.getGATKChunks(); initialize(); }
/** * Returns an approximation of the number of uncompressed bytes in this * file span. * @return Approximation of uncompressed bytes in filespan. */ public long size() { long size = 0L; for(GATKChunk chunk: getGATKChunks()) size += chunk.size(); return size; }
@Test public void testUnionOfNonOverlappingFileSpans() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,65535)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535)); GATKBAMFileSpan union = regionOne.union(regionTwo); Assert.assertEquals(union.getGATKChunks().size(),2,"Discontiguous elements were merged"); Assert.assertEquals(union.getGATKChunks().get(0),regionOne.getGATKChunks().get(0),"Wrong chunk was first in list"); Assert.assertEquals(union.getGATKChunks().get(1),regionTwo.getGATKChunks().get(0),"Wrong chunk was second in list"); }
@Test public void testUnionOfEmptyFileSpans() { GATKBAMFileSpan empty1 = new GATKBAMFileSpan(); GATKBAMFileSpan empty2 = new GATKBAMFileSpan(); GATKBAMFileSpan union = empty1.union(empty2); Assert.assertEquals(union.getGATKChunks().size(),0,"Elements inserted in union of two empty sets"); }
@Test public void testIntersectionOfStrictSubset() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,2<<16)); GATKBAMFileSpan intersection = regionOne.intersection(regionTwo); Assert.assertEquals(intersection.getGATKChunks().size(),1,"No intersection found between two partially overlapping filespans"); Assert.assertEquals(intersection.getGATKChunks().get(0),new GATKChunk(0<<16,1<<16),"Determined intersection is incorrect."); // Make sure intersection is symmetric intersection = regionTwo.intersection(regionOne); Assert.assertEquals(intersection.getGATKChunks().size(),1,"No intersection found between two partially overlapping filespans"); Assert.assertEquals(intersection.getGATKChunks().get(0),new GATKChunk(0<<16,1<<16),"Determined intersection is incorrect."); }
@Test public void testIntersectionOfEmptyFileSpans() { GATKBAMFileSpan empty1 = new GATKBAMFileSpan(); GATKBAMFileSpan empty2 = new GATKBAMFileSpan(); GATKBAMFileSpan intersection = empty1.intersection(empty2); Assert.assertEquals(intersection.getGATKChunks().size(),0,"Elements inserted in intersection of two empty sets"); }
@Test public void testUnionOfFileSpansFirstRegionEndsWithinSecondRegion() { // Region 1 ends within Region 2: // |---2----| // |---1----| GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,(1<<16)|32767)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535)); GATKBAMFileSpan union = regionOne.union(regionTwo); Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not."); Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,(1<<16)|65535)); }
@Test public void testUnionOfFileSpansFirstRegionEndsAtSecondRegionEnd() { // Region 1 ends at Region 2 end: // |---2----| // |---1-----------| GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,(1<<16)|65535)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535)); GATKBAMFileSpan union = regionOne.union(regionTwo); Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not."); Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,(1<<16)|65535)); }
@Test public void testUnionOfFileSpansFirstRegionEndsAfterSecondRegionEnd() { // Region 1 ends after Region 2 end: // |---2----| // |---1---------------| GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,(1<<16)|65535)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|32767)); GATKBAMFileSpan union = regionOne.union(regionTwo); Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not."); Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,(1<<16)|65535)); }
@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 testUnionOfContiguousFileSpans() { // Region 1 ends at position adjacent to Region 2 start: // |---1----|---2----| GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535)); GATKBAMFileSpan union = regionOne.union(regionTwo); Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not."); Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,(1<<16)|65535)); }
@Test public void testUnionOfFileSpansFirstRegionStartsAtSecondRegionStart() { // Region 1 starts at Region 2 start, but ends before Region 2: // |---2--------| // |---1----| GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|32767)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535)); GATKBAMFileSpan union = regionOne.union(regionTwo); Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not."); Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(1<<16,(1<<16)|65535)); }
@Test public void testUnionOfFileSpansFirstRegionEqualToSecondRegion() { // Region 1 and Region 2 represent the same region: // |---2----| // |---1----| GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535)); GATKBAMFileSpan union = regionOne.union(regionTwo); Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not."); Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(1<<16,(1<<16)|65535)); }
@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 testIntersectionOfPartialOverlap() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0<<16|32768,1<<16|32768)); GATKBAMFileSpan intersection = regionOne.intersection(regionTwo); Assert.assertEquals(intersection.getGATKChunks().size(),1,"No intersection found between two partially overlapping filespans"); Assert.assertEquals(intersection.getGATKChunks().get(0),new GATKChunk(0<<16|32768,1<<16|32768),"Determined intersection is incorrect."); }
@Test public void testUnionAllFileSpansAdded() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16), new GATKChunk(20<<16,21<<16) }); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,2<<16)); GATKBAMFileSpan union = regionOne.union(regionTwo); Assert.assertEquals(union.getGATKChunks().size(),2,"Elements to be merged were not."); Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,3<<16)); Assert.assertEquals(union.getGATKChunks().get(1),new GATKChunk(20<<16,21<<16)); }
@Test public void testUnionOfStringOfFileSpans() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) }); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,2<<16)); GATKBAMFileSpan union = regionOne.union(regionTwo); Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not."); Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,3<<16)); }
@Test public void testIntersectionOfNonOverlappingFileSpans() { GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,2<<16)); GATKBAMFileSpan intersection = regionOne.intersection(regionTwo); Assert.assertEquals(intersection.getGATKChunks().size(),0,"Elements inserted in intersection of two non-intersecting filespans"); }
@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"); }