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Merge pull request #1452 from broadinstitute/pf_excludeIntervalPadding 

addresses issue #1280 now interval padding works for exclude intervals
This commit is contained in:
Peter Fan 2016-08-17 13:15:15 -04:00 committed by GitHub
parent 27e56b2bb9 3510906c7f
commit 01fdb90096
2 changed files with 13 additions and 1 deletions
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12
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -88,6 +88,18 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testDiscordanceNoSampleSpecified--" + testFile, spec);
}
@Test
public void testExcludeIntervalsPadding(){
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -L 1:1715011-1734970 -XL 1:1725305 -ip 200 --variant "
+ b37hapmapGenotypes + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("2e31c0be0d639d7110e639a11c03f4ca")
);
executeTest("testExcludeIntervalsPadding--", spec);
}
@Test
public void testRepeatedLineSelection() {
String testfile = privateTestDir + "test.dup.vcf";

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

@ -658,7 +658,7 @@ public class IntervalUtils {
GenomeLocSortedSet excludeSortedSet = null;
if (excludeIntervals != null && excludeIntervals.size() > 0) {
excludeSortedSet = loadIntervals(excludeIntervals, IntervalSetRule.UNION, intervalMergingRule, 0, genomeLocParser);
excludeSortedSet = loadIntervals(excludeIntervals, IntervalSetRule.UNION, intervalMergingRule, intervalPadding, genomeLocParser);
}
return new Pair<GenomeLocSortedSet, GenomeLocSortedSet>(includeSortedSet, excludeSortedSet);
}