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Did some refactoring which broke some unit tests, and then failed to run 

the unit tests.  Definitely not my best effort...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5599 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-04-08 03:31:52 +00:00
parent 74755cfd1c
commit 53db7b8faa
1 changed files with 5 additions and 5 deletions
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10
java/test/net/sf/samtools/GATKBAMFileSpanUnitTest.java
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@ -145,7 +145,7 @@ public class GATKBAMFileSpanUnitTest {
public void testSubtractionOfEmptyChunkLists() { public void testSubtractionOfEmptyChunkLists() {
GATKBAMFileSpan regionOne = new GATKBAMFileSpan(); GATKBAMFileSpan regionOne = new GATKBAMFileSpan();
GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan();
GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo); GATKBAMFileSpan subtraction = regionOne.minus(regionTwo);
Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in subtraction of two empty sets"); Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in subtraction of two empty sets");
} }
@ -153,7 +153,7 @@ public class GATKBAMFileSpanUnitTest {
public void testSingleIntervalSubtractedAway() { public void testSingleIntervalSubtractedAway() {
GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16)); GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,1<<16)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo); GATKBAMFileSpan subtraction = regionOne.minus(regionTwo);
Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in complete subtraction of region"); Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in complete subtraction of region");
} }
@ -161,7 +161,7 @@ public class GATKBAMFileSpanUnitTest {
public void testMultipleIntervalsSubtractedAway() { public void testMultipleIntervalsSubtractedAway() {
GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) }); 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 regionTwo = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) });
GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo); GATKBAMFileSpan subtraction = regionOne.minus(regionTwo);
Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in complete subtraction of region"); Assert.assertEquals(subtraction.getGATKChunks().size(),0,"Elements inserted in complete subtraction of region");
} }
@ -169,7 +169,7 @@ public class GATKBAMFileSpanUnitTest {
public void testSubtractionOfStrictSubset() { public void testSubtractionOfStrictSubset() {
GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16)); GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16));
GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,1<<16)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo); GATKBAMFileSpan subtraction = regionOne.minus(regionTwo);
Assert.assertEquals(subtraction.getGATKChunks().size(),1,"Incorrect size in strict subset subtraction of region"); 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."); Assert.assertEquals(subtraction.getGATKChunks().get(0),new GATKChunk(1<<16,2<<16),"Determined subtraction is incorrect.");
} }
@ -178,7 +178,7 @@ public class GATKBAMFileSpanUnitTest {
public void testSubtractionOfPartialOverlap() { public void testSubtractionOfPartialOverlap() {
GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16)); GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,2<<16));
GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,3<<16)); GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,3<<16));
GATKBAMFileSpan subtraction = regionOne.subtract(regionTwo); GATKBAMFileSpan subtraction = regionOne.minus(regionTwo);
Assert.assertEquals(subtraction.getGATKChunks().size(),1,"Incorrect size in partial subset subtraction of region"); 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."); Assert.assertEquals(subtraction.getGATKChunks().get(0),new GATKChunk(0<<16,1<<16),"Determined subtraction is incorrect.");
} }