- Fixed output for beagle header
- Better description for QualByDepth annotation git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2655 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
d9df72e1b5
commit
c1e09efb23
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@ -34,7 +34,7 @@ public class QualByDepth extends StandardVariantAnnotation {
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public String getKeyName() { return "QD"; }
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public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine(getKeyName(), 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Genotype Quality by Depth"); }
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public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine(getKeyName(), 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Variant Confidence/Quality by Depth"); }
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private int variationQualByDepth(char ref, final List<Genotype> genotypes, Map<String, StratifiedAlignmentContext> stratifiedContexts) {
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int depth = 0;
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@ -141,10 +141,8 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
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}
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if ( beagleWriter != null ) {
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beagleWriter.print("marker alleleA alleleB");
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for ( String sample : samples ) {
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beagleWriter.print(' ');
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beagleWriter.print(sample);
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}
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for ( String sample : samples )
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beagleWriter.print(String.format(" %s %s %s", sample, sample, sample));
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beagleWriter.println();
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}
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@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("514d6357ae4970a422d0481f57f52e0c"));
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Arrays.asList("36aaac8c38480b7f49766b8b88f9c537"));
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executeTest("test file has annotations, asking for annotations, #1", spec);
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}
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@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("903c0a9642a34ed19dadee72ddcf4189"));
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Arrays.asList("74d1dc2a65f4398cd8c11b294917dfe5"));
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executeTest("test file has annotations, asking for annotations, #2", spec);
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}
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@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("90861b8af4514f8e64e4d93fe0fcd304"));
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Arrays.asList("9fc6e8c5ee56a67f158bbf305470643d"));
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executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
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}
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@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("0e9c65b14ef694bb3f246e58515dbdce"));
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Arrays.asList("857875a3234112bcd047cf31683aa331"));
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executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
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}
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@ -22,7 +22,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot1PointEM() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "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,
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Arrays.asList("4a3967d7ebcea2a5ba36882b7338397a"));
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Arrays.asList("46232790dae2e99e79626de78836ba08"));
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executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
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}
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@ -30,7 +30,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot2PointEM() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "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,
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Arrays.asList("f00e37b4943246b852b666cc066fbb45"));
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Arrays.asList("683cfa48cc5e2d140286645873184c20"));
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executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
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}
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@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testPooled1() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
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Arrays.asList("446560ea66de1a62269be6375c45ca93"));
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Arrays.asList("f2b3799fe18010aa8cfd76b0e0782db7"));
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executeTest("testPooled1", spec);
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}
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@ -56,7 +56,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot1Joint() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
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Arrays.asList("b49c59ec1b3315c983de5e0d27079d82"));
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Arrays.asList("42fc8d585f2f30dc6c58d413738e1f7c"));
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executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
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}
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@ -64,7 +64,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot2Joint() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
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Arrays.asList("3f86d2eaae6474565fdff3c314d34042"));
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Arrays.asList("c854552bbf4a33b8dca488ea5f0a4a32"));
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executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
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}
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@ -72,7 +72,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testSingleSamplePilot2Joint() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
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Arrays.asList("4cdd7b4ed1bf287e4ccec6cc460f0b50"));
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Arrays.asList("9dcb1d4af7c02804150a0f6c38be4e1e"));
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executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
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}
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@ -85,7 +85,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testParallelization() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,400,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 -nt 4", 1,
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Arrays.asList("0b4b1c25150b779f0e6bc52a4cbbd8c2"));
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Arrays.asList("35637b1ec52f2a7c0551b87795c3060c"));
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executeTest("test parallelization", spec);
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}
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@ -98,11 +98,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testParameter() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( "-genotype", "cad3a34b66c0c95210a3c554410f8a38" );
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e.put( "-all_bases", "83a1baa9807b367f3437748627d3fec6" );
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e.put( "--min_base_quality_score 26", "46589944cdd7162e24db9bdac22842eb" );
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e.put( "--min_mapping_quality_score 26", "db18b1336fc1351d8bc95b677873e75f" );
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e.put( "--max_mismatches_in_40bp_window 5", "374e23d647d309ff1df1653aea83aa83" );
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e.put( "-genotype", "e5d4287d27aa7734f0d57a8213f549ef" );
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e.put( "-all_bases", "3a291bb06764e3615230f467cc501096" );
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e.put( "--min_base_quality_score 26", "fb00499f249973c156ca64e30e7b2d91" );
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e.put( "--min_mapping_quality_score 26", "315c7951a783655445933ed9d83db2c2" );
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e.put( "--max_mismatches_in_40bp_window 5", "bca61f8afce9f64763a1225e9c614d38" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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@ -116,7 +116,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testConfidence() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10 ", 1,
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Arrays.asList("5c420264fa1661259170b0f98be5439a"));
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Arrays.asList("c7427818f57cc3bf11e9ee98461c1a65"));
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executeTest("testConfidence", spec);
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}
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@ -212,7 +212,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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// --------------------------------------------------------------------------------------------------------------
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@Test
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public void testOtherOutput() {
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String[] md5s = {"a5dce541f00d3fe364d110f1cae53538", "cea954546a304aa98fc3a18d4305090a"};
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String[] md5s = {"a5dce541f00d3fe364d110f1cae53538", "0147670a1b62bb3d218d5ed3f9fc4656"};
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper" +
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" -R " + oneKGLocation + "reference/human_b36_both.fasta" +
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