Un-exclude SD and TRA from HC annotators; resolves #966

Exclude MQ0BySample Move SD and TRA to new StandardUGAnnotation interface There is now annotation interface (StandardUGAnnotation) holding annots that are standard in UG but should't be used as they are now with HC. This allows us to not have to exclude these annotations explicitly in HC, but still be able to use them for development purposes.
2015-05-01 22:15:00 +02:00 · 2015-05-01 22:15:00 +02:00 · 071d82d1bf
parent e49f6dfd0f
commit 071d82d1bf
6 changed files with 51 additions and 22 deletions
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SpanningDeletions.java
@ -55,7 +55,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardUGAnnotation;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
@ -76,12 +76,12 @@ import java.util.*;
 *
 * <h3>Caveats</h3>
 * <ul>
- *     <li>This annotation is not compatible with HaplotypeCaller; its purpose is to compensate for the UnifiedGenotyper's inability to integrate SNPs and indels in the same model (unlike HaplotypeCaller)</li>
+ *     <li>In its current form, this annotation is not compatible with HaplotypeCaller. It is only meant to be used with UnifiedGenotyper, as its purpose is to compensate for the UnifiedGenotyper's inability to integrate SNPs and indels in the same model (unlike HaplotypeCaller).</li>
 *     <li>By default, the UnifiedGenotyper will not call variants where the fraction of spanning deletions is above a certain threshold. This threshold can be adjusted using the `--max_deletion_fraction` argument.</li>
 * </ul>
 *
 */
-public class SpanningDeletions extends InfoFieldAnnotation implements StandardAnnotation {
+public class SpanningDeletions extends InfoFieldAnnotation implements StandardUGAnnotation {

    private final static Logger logger = Logger.getLogger(SpanningDeletions.class);
    private boolean walkerIdentityCheckWarningLogged = false;
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java
@ -58,7 +58,7 @@ import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardUGAnnotation;
 import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
@ -76,13 +76,13 @@ import java.util.*;
 *
 * <p>A tandem repeat unit is composed of one or more nucleotides that are repeated multiple times in series. Repetitive sequences are difficult to map to the reference because they are associated with multiple alignment possibilities. Knowing the number of repeat units in a set of tandem repeats tells you the number of different positions the tandem repeat can be placed in. The observation of many tandem repeat units multiplies the number of possible representations that can be made of the region.
 *
- * <h3>Caveats</h3>
+ * <h3>Caveat</h3>
 * <ul>
 *     <li>This annotation is currently not compatible with HaplotypeCaller.</li>
 * </ul>
 *
 */
-public class TandemRepeatAnnotator extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
+public class TandemRepeatAnnotator extends InfoFieldAnnotation implements StandardUGAnnotation, ActiveRegionBasedAnnotation {
    private final static Logger logger = Logger.getLogger(TandemRepeatAnnotator.class);
    private boolean walkerIdentityCheckWarningLogged = false;

--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java
@ -219,7 +219,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
     * Keep in mind that RODRequiringAnnotations are not intended to be used as a group, because they require specific ROD inputs.
     */
    @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls.  The single value 'none' removes the default group", required=false)
-    protected String[] annotationClassesToUse = { "Standard" };
+    protected String[] annotationClassesToUse = { "Standard", "StandardUG" };

    // the calculation arguments
    private UnifiedGenotypingEngine genotypingEngine = null;
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@ -298,7 +298,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     */
    @Advanced
    @Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
-    protected List<String> annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{"SpanningDeletions", "TandemRepeatAnnotator", "MappingQualityZero"}));
+    protected List<String> annotationsToExclude = new ArrayList<>(Arrays.asList(new String[]{"MappingQualityZero", "MappingQualityZeroBySample"}));

    /**
     * Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
@ -74,6 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {

    final static String REF = b37KGReference;
    final static String CEUTRIO_BAM = validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
+    final static String standardAnnotations = " -G Standard -G StandardUG ";

    public static String baseTestString() {
        return "-T VariantAnnotator -R " + b36KGReference + " --no_cmdline_in_header -o %s";
@ -98,7 +99,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testHasAnnotsAsking1() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                Arrays.asList("92eb47332dd9d7ee7fbe3120dc39c594"));
        executeTest("test file has annotations, asking for annotations, #1", spec);
    }
@ -106,7 +107,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testHasAnnotsAsking2() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                Arrays.asList("c367bf7cebd7b26305f8d4736788aec8"));
        executeTest("test file has annotations, asking for annotations, #2", spec);
    }
@ -132,7 +133,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testNoAnnotsAsking1() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                Arrays.asList("098dcad8d90d90391755a0191c9db59c"));
        executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
    }
@ -140,7 +141,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testNoAnnotsAsking2() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                Arrays.asList("f3bbfbc179d2e1bae49890f1e9dfde34"));
        executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
    }
@ -148,7 +149,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testExcludeAnnotations() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + standardAnnotations + "-XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                Arrays.asList("7267450fc4d002f75a24ca17278e0950"));
        executeTest("test exclude annotations", spec);
    }
@ -181,7 +182,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testOverwritingHeader() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
+                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
                Arrays.asList("18592c72d83ee84e1326acb999518c38"));
        executeTest("test overwriting header", spec);
    }
@ -189,7 +190,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testNoReads() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
                Arrays.asList("6de950b381d2d92b21bab6144e8f0714"));
        executeTest("not passing it any reads", spec);
    }
@ -197,7 +198,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testDBTagWithDbsnp() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                baseTestString() + " --dbsnp " + b36dbSNP129 + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
                Arrays.asList("e0bd85747c87ea4df6ef67f593cbacbf"));
        executeTest("getting DB tag with dbSNP", spec);
    }
@ -205,7 +206,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testMultipleIdsWithDbsnp() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
+                baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + standardAnnotations + "--variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
                Arrays.asList("194a942f17104292192fb564a3c96610"));
        executeTest("adding multiple IDs with dbSNP", spec);
    }
@ -213,7 +214,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testDBTagWithHapMap() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
                Arrays.asList("9e41ae733a76632b40eda38e3cef909d"));
        executeTest("getting DB tag with HM3", spec);
    }
@ -221,7 +222,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testDBTagWithTwoComps() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf " + standardAnnotations + " --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
                Arrays.asList("7b718bae0444f1896a6e86da80531218"));
        executeTest("getting DB tag with 2 comps", spec);
    }
@ -237,7 +238,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testUsingExpression() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
                Arrays.asList("0bed7b4f6ed0556c5e7d398353a9fa91"));
        executeTest("using expression", spec);
    }
@ -245,7 +246,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testUsingExpressionMultiAllele() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
+                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
                Arrays.asList("195cf0f5b1aa5c7d00a0595dcca02f4c"));
        executeTest("using expression with multi-alleles", spec);
    }
@ -253,7 +254,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
    @Test
    public void testUsingExpressionWithID() {
        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
+                baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
                Arrays.asList("b3fe9d3bdb18ca2629543f849a7d27ed"));
        executeTest("using expression with ID", spec);
    }
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java
@ -0,0 +1,28 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+*
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+*
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+*
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
+
+public interface StandardUGAnnotation extends AnnotationType {}