zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Minor fixups for previous commit once tests (only runnable at Broad) were run. 

Fixed off by one error in size calculation IntervalUtils.scatterContigIntervals().
In test for fewer files than intervals, adjusted expected intervals.
In test for more files than intervals, adjusted expected exception.
This commit is contained in:
Khalid Shakir 2014-10-22 17:37:37 +08:00
parent a62dc84795
commit 26ba4c11aa
2 changed files with 7 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java
View File

@ -371,7 +371,7 @@ public class IntervalUtils {
long totalBases = 0;
for(GenomeLoc loc : locs)
totalBases += loc.getStop() - loc.getStart();
totalBases += loc.size();
long idealBasesPerPart = totalBases / scatterParts.size();
if(idealBasesPerPart == 0)

12
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java
View File

@ -671,17 +671,17 @@ public class IntervalUtilsUnitTest extends BaseTest {
List<GenomeLoc> locs2 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(1).toString()));
List<GenomeLoc> locs3 = IntervalUtils.parseIntervalArguments(hg18GenomeLocParser, Arrays.asList(files.get(2).toString()));
Assert.assertEquals(locs1.size(), 1);
Assert.assertEquals(locs1.size(), 2);
Assert.assertEquals(locs2.size(), 1);
Assert.assertEquals(locs3.size(), 2);
Assert.assertEquals(locs3.size(), 1);
Assert.assertEquals(locs1.get(0), chr1);
Assert.assertEquals(locs2.get(0), chr2);
Assert.assertEquals(locs3.get(0), chr3);
Assert.assertEquals(locs3.get(1), chr4);
Assert.assertEquals(locs1.get(1), chr2);
Assert.assertEquals(locs2.get(0), chr3);
Assert.assertEquals(locs3.get(0), chr4);
}
@Test(expectedExceptions=UserException.BadArgumentValue.class)
@Test(expectedExceptions=UserException.BadInput.class)
public void testScatterContigIntervalsMoreFiles() {
List<File> files = testFiles("contig_more.", 3, ".intervals");
IntervalUtils.scatterContigIntervals(hg18Header, getLocs("chr1", "chr2"), files);