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When called as a standalone, VariantAnnotator now emits samples in sorted (as opposed to random) order in VCFs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2392 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-17 19:01:08 +00:00
parent aa86f3710d
commit c75ec67f84
2 changed files with 5 additions and 5 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -82,7 +82,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
listFiltersAndExit();
// get the list of all sample names from the various VCF input rods
HashSet<String> samples = new HashSet<String>();
TreeSet<String> samples = new TreeSet<String>();
VCFUtils.getUniquifiedSamplesFromRods(getToolkit(), samples, new HashMap<Pair<String, String>, String>());
// add the non-VCF sample from the command-line, if applicable

8
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -50,7 +50,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("6903f8b31820ce7a56230b99f9a9309c"));
Arrays.asList("5c73e85a91bf8f8e9c47c445ec77233c"));
executeTest("test file has annotations, not asking for annotations, #1", spec);
}
@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("d9f623b69e20b9c6289562f123b867eb"));
Arrays.asList("2d3e220e96eb00c4c7bb2dbc8353d9bd"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("b46f395864cb71b887d69342f56e7fdb"));
Arrays.asList("acef97201f2d17007dbdee6c639536ea"));
executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
}
@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("23928a3f79fd5d841505cdeaf342c8dc"));
Arrays.asList("2031599f8554d16342f53cb80fae296a"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}