186 lines
10 KiB
Java
186 lines
10 KiB
Java
/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package net.sf.samtools;
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import org.testng.Assert;
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import org.testng.annotations.Test;
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/**
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* Tests of functionality of union, intersection operators.
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*/
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public class GATKBAMFileSpanUnitTest {
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@Test
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public void testUnionOfEmptyFileSpans() {
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GATKBAMFileSpan empty1 = new GATKBAMFileSpan();
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GATKBAMFileSpan empty2 = new GATKBAMFileSpan();
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GATKBAMFileSpan union = empty1.union(empty2);
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Assert.assertEquals(union.getGATKChunks().size(),0,"Elements inserted in union of two empty sets");
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}
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@Test
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public void testUnionOfNonOverlappingFileSpans() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,65535));
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535));
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GATKBAMFileSpan union = regionOne.union(regionTwo);
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Assert.assertEquals(union.getGATKChunks().size(),2,"Discontiguous elements were merged");
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Assert.assertEquals(union.getGATKChunks().get(0),regionOne.getGATKChunks().get(0),"Wrong chunk was first in list");
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Assert.assertEquals(union.getGATKChunks().get(1),regionTwo.getGATKChunks().get(0),"Wrong chunk was second in list");
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}
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@Test
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public void testUnionOfOverlappingFileSpans() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535));
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GATKBAMFileSpan union = regionOne.union(regionTwo);
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Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not.");
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Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,(1<<16)|65535));
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}
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@Test
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public void testUnionOfStringOfFileSpans() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) });
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,2<<16));
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GATKBAMFileSpan union = regionOne.union(regionTwo);
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Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not.");
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Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,3<<16));
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}
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@Test
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public void testUnionAllFileSpansAdded() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16), new GATKChunk(20<<16,21<<16) });
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,2<<16));
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GATKBAMFileSpan union = regionOne.union(regionTwo);
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Assert.assertEquals(union.getGATKChunks().size(),2,"Elements to be merged were not.");
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Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,3<<16));
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Assert.assertEquals(union.getGATKChunks().get(1),new GATKChunk(20<<16,21<<16));
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}
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@Test
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public void testIntersectionOfEmptyFileSpans() {
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GATKBAMFileSpan empty1 = new GATKBAMFileSpan();
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GATKBAMFileSpan empty2 = new GATKBAMFileSpan();
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GATKBAMFileSpan intersection = empty1.intersection(empty2);
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Assert.assertEquals(intersection.getGATKChunks().size(),0,"Elements inserted in intersection of two empty sets");
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}
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@Test
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public void testIntersectionOfNonOverlappingFileSpans() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,2<<16));
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GATKBAMFileSpan intersection = regionOne.intersection(regionTwo);
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Assert.assertEquals(intersection.getGATKChunks().size(),0,"Elements inserted in intersection of two non-intersecting filespans");
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}
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@Test
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public void testIntersectionOfSmallOverlapInFileSpans() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(65535,2<<16));
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GATKBAMFileSpan intersection = regionOne.intersection(regionTwo);
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Assert.assertEquals(intersection.getGATKChunks().size(),1,"No intersection found between two partially overlapping filespans");
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Assert.assertEquals(intersection.getGATKChunks().get(0),new GATKChunk(65535,1<<16),"Determined intersection is incorrect.");
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}
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@Test
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public void testIntersectionOfStrictSubset() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,2<<16));
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GATKBAMFileSpan intersection = regionOne.intersection(regionTwo);
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Assert.assertEquals(intersection.getGATKChunks().size(),1,"No intersection found between two partially overlapping filespans");
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Assert.assertEquals(intersection.getGATKChunks().get(0),new GATKChunk(0<<16,1<<16),"Determined intersection is incorrect.");
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// Make sure intersection is symmetric
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intersection = regionTwo.intersection(regionOne);
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Assert.assertEquals(intersection.getGATKChunks().size(),1,"No intersection found between two partially overlapping filespans");
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Assert.assertEquals(intersection.getGATKChunks().get(0),new GATKChunk(0<<16,1<<16),"Determined intersection is incorrect.");
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}
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@Test
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public void testIntersectionOfPartialOverlap() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16));
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0<<16|32768,1<<16|32768));
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GATKBAMFileSpan intersection = regionOne.intersection(regionTwo);
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Assert.assertEquals(intersection.getGATKChunks().size(),1,"No intersection found between two partially overlapping filespans");
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Assert.assertEquals(intersection.getGATKChunks().get(0),new GATKChunk(0<<16|32768,1<<16|32768),"Determined intersection is incorrect.");
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}
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@Test
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public void testIntersectionOfChunkLists() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,5<<16));
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(1<<16,2<<16), new GATKChunk(3<<16,4<<16) });
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GATKBAMFileSpan intersection = regionOne.intersection(regionTwo);
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Assert.assertEquals(intersection.getGATKChunks().size(),2,"Wrong number of intersections found.");
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Assert.assertEquals(intersection.getGATKChunks().get(0),new GATKChunk(1<<16,2<<16),"Determined intersection is incorrect.");
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Assert.assertEquals(intersection.getGATKChunks().get(1),new GATKChunk(3<<16,4<<16),"Determined intersection is incorrect.");
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// Make sure intersection is symmetric
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intersection = regionTwo.intersection(regionOne);
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Assert.assertEquals(intersection.getGATKChunks().size(),2,"Wrong number of intersections found.");
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Assert.assertEquals(intersection.getGATKChunks().get(0),new GATKChunk(1<<16,2<<16),"Determined intersection is incorrect.");
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Assert.assertEquals(intersection.getGATKChunks().get(1),new GATKChunk(3<<16,4<<16),"Determined intersection is incorrect.");
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}
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@Test
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public void testSubtractionOfEmptyChunkLists() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan();
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan();
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GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo);
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Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in subtraction of two empty sets");
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}
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@Test
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public void testSingleIntervalSubtractedAway() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
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GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo);
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Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in complete subtraction of region");
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}
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@Test
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public void testMultipleIntervalsSubtractedAway() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) });
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) });
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GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo);
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Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in complete subtraction of region");
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}
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@Test
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public void testSubtractionOfStrictSubset() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16));
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
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GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo);
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Assert.assertEquals(subtraction.getGATKChunks().size(),1,"Incorrect size in strict subset subtraction of region");
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Assert.assertEquals(subtraction.getGATKChunks().get(0),new GATKChunk(1<<16,2<<16),"Determined subtraction is incorrect.");
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}
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@Test
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public void testSubtractionOfPartialOverlap() {
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GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16));
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GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,3<<16));
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GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo);
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Assert.assertEquals(subtraction.getGATKChunks().size(),1,"Incorrect size in partial subset subtraction of region");
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Assert.assertEquals(subtraction.getGATKChunks().get(0),new GATKChunk(0<<16,1<<16),"Determined subtraction is incorrect.");
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}
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}
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