From a74e571fe24975d86c9a447f9f6b6f04c61ea268 Mon Sep 17 00:00:00 2001
From: Ron Levine <ron.how.levine@gmail.com>
Date: Fri, 11 Jan 2019 13:55:53 -0500
Subject: [PATCH] Add warning message to add allele specific annotation group
 (#3042)

---
 .../walkers/ReferenceConfidenceVariantContextMerger.java      | 4 ++++
 .../hellbender/utils/variant/GATKVCFConstants.java            | 1 +
 .../org/broadinstitute/hellbender/testutils/BaseTest.java     | 2 +-
 3 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java
index 6e60578b026..6163cfa53ed 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/ReferenceConfidenceVariantContextMerger.java
@@ -34,6 +34,7 @@ public final class ReferenceConfidenceVariantContextMerger {
     protected final VariantAnnotatorEngine annotatorEngine;
     protected final OneShotLogger oneShotAnnotationLogger = new OneShotLogger(this.getClass());
     protected final OneShotLogger oneShotHeaderLineLogger = new OneShotLogger(this.getClass());
+    protected final OneShotLogger AS_Warning = new OneShotLogger(this.getClass());
 
     public ReferenceConfidenceVariantContextMerger(VariantAnnotatorEngine engine, final VCFHeader inputHeader) {
         Utils.nonNull(inputHeader, "A VCF header must be provided");
@@ -391,6 +392,9 @@ private void addReferenceConfidenceAttributes(final VCWithNewAlleles vcPair, fin
                     values.add(parseNumericInfoAttributeValue(vcfInputHeader, key, value.toString()));
                 } catch (final NumberFormatException e) {
                     oneShotAnnotationLogger.warn(String.format("Detected invalid annotations: When trying to merge variant contexts at location %s:%d the annotation %s was not a numerical value and was ignored",vcPair.getVc().getContig(),vcPair.getVc().getStart(),p.toString()));
+                    if (key.startsWith(GATKVCFConstants.ALLELE_SPECIFIC_ANNOTATION_PREFIX)) {
+                        AS_Warning.warn(String.format("Reducible annotation '%s' detected, add -G Standard -G AS_Standard to the command to annotate in the final VC with this annotation.",key));
+                    }
                 }
             }
         }
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
index 1ed02d90f2c..c54237321c7 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
@@ -185,6 +185,7 @@ their names (or descriptions) depend on some threshold.  Those filters are not i
     public final static String NON_REF_SYMBOLIC_ALLELE_NAME = "NON_REF";
     public final static String SPANNING_DELETION_SYMBOLIC_ALLELE_NAME_DEPRECATED = "*:DEL";
     public final static Allele SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED = Allele.create("<" + SPANNING_DELETION_SYMBOLIC_ALLELE_NAME_DEPRECATED + ">", false); // represents any possible spanning deletion allele at this si
+    public static final String ALLELE_SPECIFIC_ANNOTATION_PREFIX = "AS";
 
 
     public static boolean isSpanningDeletion(final Allele allele){
diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java
index 787dd7b3ccc..306b1598442 100644
--- a/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java
+++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java
@@ -394,7 +394,7 @@ private static String captureSystemStream(Runnable runnable,  PrintStream stream
     }
 
     public static void assertContains(String actual, String expectedSubstring){
-        Assert.assertTrue(actual.contains(expectedSubstring),  expectedSubstring +" was not found in " + actual+ ".");
+        Assert.assertTrue(actual.contains(expectedSubstring),  expectedSubstring +" was not found in " + actual + ".");
     }
 
     public static <T> void assertCondition(Iterable<T> actual, Iterable<T> expected, BiConsumer<T,T> assertion){