From 58937bf9ba4a233aa3c708635bd539524ccb3c4d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 4 Dec 2009 04:45:05 +0000
Subject: [PATCH] You can now use the -exp flag to tell the Genotyper to
 include experimental annotations when it calls out to VariantAnnotator.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2256 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/annotator/VariantAnnotator.java   | 9 +++++++++
 .../walkers/genotyper/UnifiedArgumentCollection.java     | 3 +++
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java   | 6 +++++-
 3 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index b15ce33dc..85d9ecfc1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -176,12 +176,21 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         return 1;
     }
 
+    // option #1: don't specify annotations to be used: standard annotations are used by default
     public static Map<String, String> getAnnotations(ReferenceContext ref, AlignmentContext context, Variation variation, List<Genotype> genotypes) {
         if ( standardAnnotations == null )
             determineAllAnnotations();
         return getAnnotations(ref, context, variation, genotypes, standardAnnotations.values());
     }
 
+    // option #2: specify that all possible annotations be used
+    public static Map<String, String> getAllAnnotations(ReferenceContext ref, AlignmentContext context, Variation variation, List<Genotype> genotypes) {
+        if ( allAnnotations == null )
+            determineAllAnnotations();
+        return getAnnotations(ref, context, variation, genotypes, allAnnotations.values());
+    }
+
+    // option #3: specify the exact annotations to be used
     public static Map<String, String> getAnnotations(ReferenceContext ref, AlignmentContext context, Variation variation, List<Genotype> genotypes, Collection<VariantAnnotation> annotations) {
 
         // set up the pileup for the full collection of reads at this position
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 873de5161..a092e2221 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -60,6 +60,9 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "noSLOD", shortName = "nsl", doc = "If provided, we will not calculate the SLOD", required = false)
     public boolean NO_SLOD = false;
 
+    @Argument(fullName = "include_experimental_annotations", shortName = "exp", doc = "Annotate calls with all annotations, including experimental ones", required = false)
+    public boolean ALL_ANNOTATIONS = false;
+
 
     // control the error modes
     @Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 26109849b..a90c75928 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -172,7 +172,11 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<Genotype>, GenotypeL
 
         // annotate the call, if possible
         if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked ) {
-            Map<String, String> annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.second, call.first);
+            Map<String, String> annotations;
+            if ( UAC.ALL_ANNOTATIONS )
+                annotations = VariantAnnotator.getAllAnnotations(refContext, fullContext, call.second, call.first);
+            else
+                annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.second, call.first);
             ((ArbitraryFieldsBacked)call.second).setFields(annotations);
         }