From df7a48233549598703bd07609d77ed57e2ced3bc Mon Sep 17 00:00:00 2001
From: Takuto Sato <tsato@broadinstitute.org>
Date: Fri, 25 Sep 2015 15:35:06 -0400
Subject: [PATCH] VariantAnnotator now supports annotating FILTER field from an
 external resource. Updated the docs.

---
 .../annotator/VariantAnnotatorIntegrationTest.java |  9 +++++++++
 .../tools/walkers/annotator/VariantAnnotator.java  | 14 ++++++++++++++
 .../walkers/annotator/VariantAnnotatorEngine.java  |  6 ++++++
 3 files changed, 29 insertions(+)

diff --git 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
index 8315a28fb..515888a09 100644
--- 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
@@ -259,6 +259,15 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         executeTest("using expression with multi-alleles", spec);
     }
 
+    @Test
+    public void testFilterInExpression(){
+        /* The order of filters in the output seems platform-dependent. May need to change htsjdk to make the order consistent across platforms. [Sato] */
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " --resource:foo " + privateTestDir + "annotationResourceWithFilter.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.FILTER -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
+                Arrays.asList("77bc144fd432b8886ab19ed20bfb9396"));
+        executeTest("annotate a vcf with the FILTER field of another vcf", spec);
+    }
+
     @Test
     public void testUsingExpressionWithID() {
         WalkerTestSpec spec = new WalkerTestSpec(
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java
index 1529ed71b..ca386e8d8 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java
@@ -97,6 +97,19 @@ import java.util.*;
  *   -E foo.AF
  *   --resourceAlleleConcordance
  * </pre>
+ *
+ * <h4>Annotate with AF and FILTER fields from an external resource </h4>
+ * <pre>
+ * java -jar GenomeAnalysisTK.jar \
+ *   -R reference.fasta \
+ *   -T VariantAnnotator \
+ *   -o output.vcf \
+ *   --resource:foo resource.vcf \
+ *   --expression foo.AF \
+ *   --expression foo.FILTER \
+ *   -V input.vcf \
+ * </pre>
+ *
  */
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
 @Requires(value={})
@@ -181,6 +194,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
      * 'resource_file.vcf', you tag it with '-resource:my_resource resource_file.vcf' (see the -resource argument, also
      * documented on this page) and you specify '-E my_resource.AC'. In the resulting output VCF, any records for
      * which there is a record at the same position in the resource file will be annotated with 'my_resource.AC=N'.
+     * INFO field data, ID, ALT, and FILTER fields may be used as expression values.
      * Note that if there are multiple records in the resource file that overlap the given position, one is chosen
      * randomly.
      */
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
index 3adcbac3f..a9d14c2ce 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
@@ -304,6 +304,12 @@ public class VariantAnnotatorEngine {
                     infoAnnotations.put(expression.fullName, expressionVC.getID());
             } else if (expression.fieldName.equals("ALT")) {
                 infoAnnotations.put(expression.fullName, expressionVC.getAlternateAllele(0).getDisplayString());
+            } else if (expression.fieldName.equals("FILTER")) {
+                if ( expressionVC.isFiltered() ) {
+                    infoAnnotations.put(expression.fullName, expressionVC.getFilters().toString().replace("[", "").replace("]", "").replace(" ", ""));
+                } else {
+                    infoAnnotations.put(expression.fullName, "PASS");
+                }
             } else if ( expressionVC.hasAttribute(expression.fieldName) ) {
                 // find the info field
                 final VCFInfoHeaderLine hInfo = hInfoMap.get(expression.fullName);