From 2cbaef2fb2bce6ce1cb816f7aa89d62b95a2eb17 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Sun, 15 Feb 2015 09:04:39 -0500
Subject: [PATCH] Throw exception for -dcov argument given to
 ActiveRegionWalkers

---
 .../HaplotypeCallerIntegrationTest.java       | 16 +++++++++++++++
 .../gatk/engine/CommandLineGATK.java          |  5 ++---
 .../gatk/engine/GenomeAnalysisEngine.java     | 20 +++++++++++++++----
 3 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index f72cf4e6f..899d23736 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -424,4 +424,20 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
                                 " -o %s",
                         1, UserException.HardwareFeatureException.class));
     }
+
+    @Test
+    public void testHaplotypeCallerDcovException(){
+        executeTest("HaplotypeCallerDcovException",
+                new WalkerTest.WalkerTestSpec(
+                        " -T HaplotypeCaller" +
+                                " --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE --maxReadsInRegionPerSample 1000 " +
+                                " --minReadsPerAlignmentStart 5 --maxProbPropagationDistance 50 --activeProbabilityThreshold 0.002 " +
+                                " --no_cmdline_in_header -minPruning 3 -pairHMM VECTOR_LOGLESS_CACHING -pairHMMSub " + HMM_SUB_IMPLEMENTATION +
+                                " -dcov 50" +
+                                " -R " + REF +
+                                " -I " + NA12878_BAM +
+                                " -L " + INTERVALS_FILE +
+                                " -o %s",
+                        1, UserException.CommandLineException.class));
+    }
 }
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
index afecc2e12..05b770005 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
@@ -203,9 +203,8 @@ public class CommandLineGATK extends CommandLineExecutable {
 
         // If no analysis name is present, fill in extra help on the walkers.
         WalkerManager walkerManager = engine.getWalkerManager();
-        String analysisName = getAnalysisName();
-        if(analysisName != null && walkerManager.exists(getAnalysisName()))
-            additionalHelp = getWalkerHelp(walkerManager.getWalkerClassByName(getAnalysisName()));
+        if(analysisName != null && walkerManager.exists(analysisName))
+            additionalHelp = getWalkerHelp(walkerManager.getWalkerClassByName(analysisName));
         else
             additionalHelp = getAllWalkerHelp();
 
diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java
index 447ceeecb..3117d3c57 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java
@@ -259,13 +259,16 @@ public class GenomeAnalysisEngine {
 
         // validate our parameters
         if (args == null) {
-            throw new ReviewedGATKException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null.");
+            throw new ReviewedGATKException("The GATKArgumentCollection passed to GenomeAnalysisEngine cannot be null.");
         }
 
         // validate our parameters              
         if (this.walker == null)
-            throw new ReviewedGATKException("The walker passed to GenomeAnalysisEngine can not be null.");
+            throw new ReviewedGATKException("The walker passed to GenomeAnalysisEngine cannot be null.");
 
+        // check that active region walkers do not use the downsampling to coverage argument
+        checkDownSamplingToCoverage();
+        
         if (args.nonDeterministicRandomSeed)
             Utils.resetRandomGenerator(System.currentTimeMillis());
 
@@ -465,8 +468,6 @@ public class GenomeAnalysisEngine {
         return this.threadAllocation == null ? 1 : threadAllocation.getTotalNumThreads();
     }
 
-
-
     /**
      * Allow subclasses and others within this package direct access to the walker manager.
      * @return The walker manager used by this package.
@@ -556,6 +557,17 @@ public class GenomeAnalysisEngine {
         checkForDuplicateSamFiles();
     }
 
+    /**
+     * Check that active region walkers do not use the downsampling to coverage argument
+     *
+     * @throws UserException if an active region walker is using the -dcov or --downsample_to_coverage downsampling arguments
+     */
+    private void checkDownSamplingToCoverage() {
+        if (argCollection.downsampleCoverage != null && walker instanceof ActiveRegionWalker) {
+            throw new UserException.CommandLineException("Cannot use -dcov or --downsample_to_coverage for ActiveRegionWalkers, use another downsampling argument");
+        }
+    }
+
     /**
      * Checks whether there are SAM files that appear multiple times in the fully unpacked list of
      * SAM files (samReaderIDs). If there are, throws an ArgumentException listing the files in question.