From 51eb95d6388d5f62e70d088fe433efda4f87bbe8 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 9 Sep 2011 11:46:37 -0400 Subject: [PATCH 1/8] Missed these tests before --- .../walkers/varianteval/VariantEvalIntegrationTest.java | 8 ++++---- .../walkers/variantutils/VCFStreamingIntegrationTest.java | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index f94c20ff6..e992684bc 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -256,7 +256,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { " --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + " --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s", - 1, Arrays.asList("2df4f8911ffc3c8d042298723ed465f8")); + 1, Arrays.asList("f70997b6a3e7fdc89d11e1d61a2463d4")); executeTestParallel("testSelect1", spec); } @@ -273,7 +273,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testCompVsEvalAC() { String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ed54aa127b173d8ad8b6482f2a929a42")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("407682de41dcf139ea635e9cda21b912")); executeTestParallel("testCompVsEvalAC",spec); } @@ -303,7 +303,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { " --dbsnp " + b37dbSNP132 + " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " -noST -ST Novelty -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("18c44636e36d6657110bf984f8eac181")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("424c9d438b1faa59b2c29413ba32f37b")); executeTestParallel("testEvalTrackWithoutGenotypes",spec); } @@ -315,7 +315,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" + " -noST -ST Novelty -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("1b8ae4fd10de0888bd843f833859d990")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("18fa0b89ebfff51141975d7e4ce7a159")); executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java index 3801e132d..00044f859 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java @@ -98,7 +98,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest { " -EV CompOverlap -noEV -noST" + " -o %s", 1, - Arrays.asList("ea09bf764adba9765b99921c5ba2c709") + Arrays.asList("d46a735ffa898f4aa6b3758c5b03f06d") ); executeTest("testVCFStreamingChain", selectTestSpec); From 60a36188453cea7e36785e80f02b7ecbbae1e779 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Fri, 9 Sep 2011 11:45:57 -0400 Subject: [PATCH 2/8] Added "alltests" build targets. To run the same set of tests as the bamboo "All Tests" plan (unit tests, integration tests, and pipeline tests): ant alltests To do the same as above on only the public portion of the codebase: ant alltests.public --- build.xml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/build.xml b/build.xml index beca6bce0..a192ab6f3 100644 --- a/build.xml +++ b/build.xml @@ -896,6 +896,18 @@ + + + + + + + + + + + + From 6bd8a53efd218857a831133e2621b9c4d5dd6375 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Fri, 9 Sep 2011 12:04:41 -0400 Subject: [PATCH 3/8] Fix nasty bug involving the build report generation when multiple test targets are specified on the same command line. Ant immutable properties: sometimes your friend, often your enemy. --- build.xml | 33 +++++++++++++++------------------ 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/build.xml b/build.xml index a192ab6f3..e5ad9daf0 100644 --- a/build.xml +++ b/build.xml @@ -821,6 +821,7 @@ + @@ -828,10 +829,6 @@ - - - - @@ -841,10 +838,10 @@ - + - - - + + - + @@ -913,7 +910,7 @@ - + @@ -921,7 +918,7 @@ - + @@ -929,7 +926,7 @@ - + @@ -937,7 +934,7 @@ - + @@ -946,24 +943,24 @@ - + - + - + - + - + From 91c949db74c3bc67e02f7bc7ef99d062ed3a0c53 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Fri, 9 Sep 2011 12:57:14 -0400 Subject: [PATCH 4/8] Fixing ValidateVariants so that it validates deletion records. Fixing GATKdocs. --- .../gatk/walkers/variantutils/ValidateVariants.java | 5 ----- .../sting/utils/variantcontext/VariantContext.java | 11 ++++++----- 2 files changed, 6 insertions(+), 10 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index 2c7902914..fdfca982c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -56,11 +56,6 @@ import java.util.Set; * A variant set to filter. *

* - *

Output

- *

- * A filtered VCF. - *

- * *

Examples

* 
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 699133e38..1c65102ae 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1085,14 +1085,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     }
 
     public void validateReferenceBases(Allele reference, Byte paddedRefBase) {
-        // don't validate if we're an insertion or complex event
-        if ( !reference.isNull() && getReference().length() == 1 && !reference.basesMatch(getReference()) ) {
-            throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
+        // don't validate if we're a complex event
+        if ( !isComplexIndel() && !reference.isNull() && !reference.basesMatch(getReference()) ) {
+            throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
         }
 
         // we also need to validate the padding base for simple indels
-        if ( hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase) )
-            throw new TribbleException.InternalCodecException(String.format("the padded REF base is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), (char)getReferenceBaseForIndel().byteValue(), (char)paddedRefBase.byteValue()));
+        if ( hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase) ) {
+            throw new TribbleException.InternalCodecException(String.format("the padded REF base is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s", getChr(), getStart(), (char)paddedRefBase.byteValue(), (char)getReferenceBaseForIndel().byteValue()));
+        }
     }
 
     public void validateRSIDs(Set rsIDs) {

From 354529bff37626c5f46de89a60987d3d3fd40aec Mon Sep 17 00:00:00 2001
From: Ryan Poplin 
Date: Fri, 9 Sep 2011 13:15:24 -0400
Subject: [PATCH 5/8] adding Validate Variants integration test with a deletion

---
 .../ValidateVariantsIntegrationTest.java             | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
index adf3b21a8..3d41be1ae 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
@@ -113,4 +113,16 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
 
         executeTest("test bad alt allele", spec);
     }
+
+    @Test
+    public void testBadAllele2() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+            baseTestString("validationExampleBad3.vcf", "ALLELES"),
+            0,
+            UserException.MalformedFile.class
+        );
+
+        executeTest("test bad alt allele", spec);
+    }
+
 }

From 1953edcd2d1a2292117cb07ff4bb0e48e2605f0e Mon Sep 17 00:00:00 2001
From: Ryan Poplin 
Date: Fri, 9 Sep 2011 13:39:08 -0400
Subject: [PATCH 6/8] updating Validate Variants deletion integration test

---
 .../walkers/variantutils/ValidateVariantsIntegrationTest.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
index 3d41be1ae..5f71f82fd 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
@@ -117,12 +117,12 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
     @Test
     public void testBadAllele2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-            baseTestString("validationExampleBad3.vcf", "ALLELES"),
+            baseTestString("validationExampleBad3.vcf", "REF"),
             0,
             UserException.MalformedFile.class
         );
 
-        executeTest("test bad alt allele", spec);
+        executeTest("test bad ref allele in deletion", spec);
     }
 
 }

From 7f9000382e4d9ef30e25739401b72e7d1a7c2fcc Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro 
Date: Fri, 9 Sep 2011 14:09:11 -0400
Subject: [PATCH 7/8] Making indel calls default in the MDCP

You can turn off indel calling by using -noIndels.
---
 .../queue/qscripts/MethodsDevelopmentCallingPipeline.scala  | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
index 80bfe03d1..17d614290 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
@@ -22,8 +22,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
   @Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false)
   var noBAQ: Boolean = false
 
-  @Argument(shortName="indels", doc="calls indels with the Unified Genotyper", required=false)
-  var callIndels: Boolean = false
+  @Argument(shortName="noIndels", doc="do not call indels with the Unified Genotyper", required=false)
+  var noIndels: Boolean = false
 
   @Argument(shortName="LOCAL_ET", doc="Doesn't use the AWS S3 storage for ET option", required=false)
   var LOCAL_ET: Boolean = false
@@ -165,7 +165,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
     val goldStandard = true
     for (target <- targets) {
       if( !skipCalling ) {
-        if (callIndels) add(new indelCall(target), new indelFilter(target), new indelEvaluation(target))
+        if (!noIndels) add(new indelCall(target), new indelFilter(target), new indelEvaluation(target))
         add(new snpCall(target))
         add(new VQSR(target, !goldStandard))
         add(new applyVQSR(target, !goldStandard))

From 9e650dfc17621a76e421184ae33b03c2515f193c Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro 
Date: Fri, 9 Sep 2011 16:25:31 -0400
Subject: [PATCH 8/8] Fixing SelectVariants documentation

getting rid of messages telling users to go for the YAML file. The idea is to not support these anymore.
---
 .../gatk/walkers/variantutils/SelectVariants.java   | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 35ff66243..018c4dcc2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -145,10 +145,9 @@ import java.util.*;
  *   -R ref.fasta \
  *   -T SelectVariants \
  *   --variant input.vcf \
- *   -o output.vcf \
- *   -SM family.yaml \
  *   -family NA12891+NA12892=NA12878 \
- *   -mvq 50
+ *   -mvq 50 \
+ *   -o violations.vcf
  *
  * Creating a sample of exactly 1000 variants randomly chosen with equal probability from the variant VCF:
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
@@ -265,17 +264,17 @@ public class SelectVariants extends RodWalker {
     private File AF_FILE = new File("");
 
     @Hidden
-    @Argument(fullName="family_structure_file", shortName="familyFile", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
+    @Argument(fullName="family_structure_file", shortName="familyFile", doc="use -family unless you know what you're doing", required=false)
     private File FAMILY_STRUCTURE_FILE = null;
 
     /**
      * String formatted as dad+mom=child where these parameters determine which sample names are examined.
      */
-    @Argument(fullName="family_structure", shortName="family", doc="Deprecated; use the -SM argument instead", required=false)
+    @Argument(fullName="family_structure", shortName="family", doc="string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
     private String FAMILY_STRUCTURE = "";
 
     /**
-     * Sample metadata information will be taken from a YAML file (see the -SM argument).
+     * This activates the mendelian violation module that will select all variants that correspond to a mendelian violation following the rules given by the family structure.
      */
     @Argument(fullName="mendelianViolation", shortName="mv", doc="output mendelian violation sites only", required=false)
     private Boolean MENDELIAN_VIOLATIONS = false;
@@ -306,7 +305,7 @@ public class SelectVariants extends RodWalker {
 
 
     @Hidden
-    @Argument(fullName="outMVFile", shortName="outMVFile", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
+    @Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false)
     private String outMVFile = null;
 
     /* Private class used to store the intermediate variants in the integer random selection process */