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The Unified Genotyper now sorts the sample names in the vcf that it outputs. 

[There was no reason to enforce that every VCF being output from the GATK should have the samples sorted, since someone might want them ordered non-alphabetically]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2102 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-20 16:13:18 +00:00
parent 38a030f2ba
commit d84444200b
2 changed files with 6 additions and 6 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -62,7 +62,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<Genotype>, GenotypeL
private GenotypeWriter writer;
// samples in input
private HashSet<String> samples;
private TreeSet<String> samples;
// keep track of some metrics about our calls
private CallMetrics callsMetrics;
@ -108,7 +108,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<Genotype>, GenotypeL
}
// get all of the unique sample names
samples = new HashSet<String>();
samples = new TreeSet<String>();
// if we're supposed to assume a single sample
if ( UAC.ASSUME_SINGLE_SAMPLE != null ) {
samples.add(UAC.ASSUME_SINGLE_SAMPLE);

8
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -47,7 +47,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1PointEM() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
Arrays.asList("37e112d619c2b6f213554edd10262523"));
Arrays.asList("fbb3ae6e835df5cf9b99dae5bf1fa8e5"));
executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
}
@ -55,7 +55,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2PointEM() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
Arrays.asList("6d28b2af631805dc593508a21ef46a83"));
Arrays.asList("98495e6f75a63558996ed45f7a1f062a"));
executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
}
@ -68,7 +68,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
Arrays.asList("3a33873d7284cc113a639ee12c925ac0"));
Arrays.asList("6f2753dbbf6b4ff98a75510e7ff2d5ae"));
executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
}
@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
Arrays.asList("bcdb54d8867543c5c316b65b27b0d3d6"));
Arrays.asList("979c1d88f2464548e83027daf685c2ad"));
executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
}