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a) Made HaplotypeScore default annotation. This changed several integration tests, whose MD5 is now updated. 

b) Disabled BaseQualRankSumTest, the returned p-values differ wildly from Matlab/R-provided ones, cause TBD.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3419 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-05-21 22:25:17 +00:00
parent f32a32269c
commit a280a0ff0d
4 changed files with 18 additions and 18 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
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@ -7,8 +7,8 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import java.util.List;
public class BaseQualityRankSumTest extends RankSumTest {
public class BaseQualityRankSumTest /*extends RankSumTest*/ {
// todo -- seems math in this test is dubious, need to recheck and verify (p-values wildly divergent from R or MATLAB)
public String getKeyName() { return "BaseQRankSum"; }
public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine("BaseQRankSum", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Phred-scaled p-value From Wilcoxon Rank Sum Test of Het Vs. Ref Base Qualities"); }

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -42,7 +42,7 @@ import java.util.*;
import net.sf.samtools.SAMRecord;
// todo -- rename to haplotype penalty
public class HaplotypeScore implements InfoFieldAnnotation, WorkInProgressAnnotation {
public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
private final static boolean DEBUG = false;
private final static int MIN_CONTEXT_WING_SIZE = 10;

8
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"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,
Arrays.asList("fb1180d956d92080c43058fd6a562385"));
Arrays.asList("08fa964f33cdf934af8cb46a9cc03ff2"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"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,
Arrays.asList("1ff5f1d3fc1a938a2763e2b9ded5db3f"));
Arrays.asList("8d57463554486cf077faf190b5af5f2d"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"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,
Arrays.asList("fb32a176d4e6df563d5d4d3ad1237baf"));
Arrays.asList("fc240f58f073071a6edf4d11b74fb493"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"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,
Arrays.asList("88edec2c057b5074e4e1ffc1ca0c2332"));
Arrays.asList("9d8b72384e90c5f8f278da9558ac2419"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}

22
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -35,7 +35,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-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", 1,
Arrays.asList("d50ebc40d935ece7e57aafc7355bec77"));
Arrays.asList("3f919977584b2c15273cb7de948dd1ac"));
executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
}
@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-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", 1,
Arrays.asList("2f113c2b1cd0d36522fc24e7784a2b7d"));
Arrays.asList("d45934ae6537a84bb123db2288ad235e"));
executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
}
@ -51,7 +51,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-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", 1,
Arrays.asList("4f08c27ada3ad1a33d12d106bc80dab6"));
Arrays.asList("96245f0842534527b66a9daad53134bd"));
executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
}
@ -64,7 +64,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testParallelization() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-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 -nt 4", 1,
Arrays.asList("d643e60343c05817dcb4fafb7870804d"));
Arrays.asList("60bf51595eda646f5ccf0b0bf5db95d8"));
executeTest("test parallelization", spec);
}
@ -77,11 +77,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-genotype", "03e228232eeb0a32ea3791daec29248c" );
e.put( "-all_bases", "fe894f335e048d89fccd7a7b39a105a1" );
e.put( "--min_base_quality_score 26", "a1142c69f1951a05d5a33215c69133af" );
e.put( "--min_mapping_quality_score 26", "796d1ea790481a1a257609279f8076bb" );
e.put( "--max_mismatches_in_40bp_window 5", "379bd56d4402e974127e0677ff51d040" );
e.put( "-genotype", "d301500f0cd5ef1929a1adce7e857f9c" );
e.put( "-all_bases", "70e94c6671a3e5122cb9ad04c0ad138e" );
e.put( "--min_base_quality_score 26", "c508728f9d26cc3a8b73f3a5ee4275f2" );
e.put( "--min_mapping_quality_score 26", "34634ea8f196eaf40dac6e069ebcf09a" );
e.put( "--max_mismatches_in_40bp_window 5", "92903b97b43145c24f19a899ce127aa3" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -95,12 +95,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
"-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 -stand_call_conf 10 ", 1,
Arrays.asList("7b41dc669e8a0abde089d7aeedab2941"));
Arrays.asList("cdcc3977ce78e15d7c8153eaf5f9a2df"));
executeTest("testConfidence1", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
"-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 -stand_emit_conf 10 ", 1,
Arrays.asList("258617b8de0e6468bf6a0c740b51676b"));
Arrays.asList("2413aafdcfd3d8ac1169662f72524035"));
executeTest("testConfidence2", spec2);
}