Addressed PR comments. GermlineCNVCaller will now throw an exception …

…if any arguments not applicable in CASE mode were set by the user.

src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java

@@ -5,6 +5,7 @@
 import org.broadinstitute.barclay.argparser.ArgumentCollection;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
+import org.broadinstitute.barclay.argparser.CommandLineArgumentParser;
 import org.broadinstitute.hellbender.cmdline.CommandLineProgram;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection;
@@ -76,6 +77,9 @@
  * diverges the second time we suggest checking if input count or karyotype values or other inputs are abnormal
  * (an example of abnormality is a count file containing mostly zeros). </p>
  *
+ * <p> More details about the model and inference procedure can be found in the white paper
+ * https://github.com/broadinstitute/gatk/blob/master/docs/CNV/germline-cnv-caller-model.pdf</p>
+ * 
  * <h3>Python environment setup</h3>
  *
  * <p>The computation done by this tool, aside from input data parsing and validation, is performed outside of the Java
@@ -121,11 +125,11 @@
  *     <dt>CASE mode:</dt>
  *     <dd><p>The tool will be run in CASE mode using the argument {@code run-mode CASE}. The path to a previously
  *     obtained model directory must be provided via the {@code model} argument in this mode. The modeled intervals are
- *     then specified by a file contained in the model directory,and all model intervals must be present in all of the
- *     input count files. All interval-related arguments (e.g. {@code interval-psi-scale} argument) are ignored in this
- *     mode, however an advanced user can adjust various sample-related (e.g. {@code sample-psi-scale}) and global
- *     (e.g. {@code p_alt}) arguments for custom applications of the tool. Inference-related (e.g.
- *     {@code min_training_epochs}) arguments can be adjusted as well. The tool output in CASE mode is only the "-calls"
+ *     then specified by a file contained in the model directory, and all model intervals must be present in all of the
+ *     input count files. All interval-related arguments (e.g. {@code interval-psi-scale}) are ignored in this
+ *     mode. However an advanced user can adjust various sample-related (e.g. {@code sample-psi-scale}) and global
+ *     (e.g. {@code p_alt}) arguments for custom applications of the tool. Inference-related arguments (e.g.
+ *     {@code min_training_epochs}) can be adjusted as well. The tool output in CASE mode is only the "-calls"
  *     subdirectory and is organized similarly to that in COHORT mode.</p>
  *
  *      <p>Note that at the moment, this tool does not automatically verify the compatibility of the provided parametrization
@@ -362,8 +366,9 @@ protected Object doWork() {
     }
 
     private void validateArguments() {
-        germlineCallingArgumentCollection.validate();
-        germlineDenoisingModelArgumentCollection.validate();
+        final CommandLineArgumentParser clpParser = (CommandLineArgumentParser) getCommandLineParser();
+        germlineCallingArgumentCollection.validate(clpParser, runMode);
+        germlineDenoisingModelArgumentCollection.validate(clpParser, runMode);
         germlineCNVHybridADVIArgumentCollection.validate();
 
         Utils.validateArg(inputReadCountPaths.size() == new HashSet<>(inputReadCountPaths).size(),

src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineCallingArgumentCollection.java

@@ -1,7 +1,10 @@
 package org.broadinstitute.hellbender.tools.copynumber.arguments;
 
+import com.google.common.collect.ImmutableList;
 import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineArgumentParser;
 import org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller;
+import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.param.ParamUtils;
 
 import java.io.Serializable;
@@ -21,6 +24,11 @@ public final class GermlineCallingArgumentCollection implements Serializable {
     public static final String CLASS_COHERENCE_LENGTH_LONG_NAME = "class-coherence-length";
     public static final String MAX_COPY_NUMBER_LONG_NAME = "max-copy-number";
 
+    // these model parameters will be extracted from provided model in CASE mode
+    private static final List<String> HIDDEN_ARGS_CASE_MODE = ImmutableList.of(
+            P_ACTIVE_LONG_NAME,
+            CLASS_COHERENCE_LENGTH_LONG_NAME);
+
     @Argument(
             doc = "Total prior probability of alternative copy-number states (the reference copy-number " +
                     "is set to the contig integer ploidy)",
@@ -78,7 +86,11 @@ public List<String> generatePythonArguments(final GermlineCNVCaller.RunMode runM
         return arguments;
     }
 
-    public void validate() {
+    public void validate(final CommandLineArgumentParser clpParser, final GermlineCNVCaller.RunMode runMode) {
+        if (runMode == GermlineCNVCaller.RunMode.CASE)
+            HIDDEN_ARGS_CASE_MODE.forEach(a -> Utils.validateArg(
+                    !clpParser.getNamedArgumentDefinitionByAlias(a).getHasBeenSet(),
+                    String.format("Argument '--%s' cannot be set in the CASE mode.", a)));
         ParamUtils.isPositive(cnvCoherenceLength,
                 String.format("Coherence length of CNV events (%s) must be positive.",
                         CNV_COHERENCE_LENGTH_LONG_NAME));

src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineDenoisingModelArgumentCollection.java

@@ -1,8 +1,12 @@
 package org.broadinstitute.hellbender.tools.copynumber.arguments;
 
+import com.google.common.collect.ImmutableList;
 import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineArgumentParser;
+import org.broadinstitute.hellbender.engine.filters.ReadFilter;
 import org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller;
 import org.broadinstitute.hellbender.utils.param.ParamUtils;
+import org.broadinstitute.hellbender.utils.Utils;
 
 import java.io.Serializable;
 import java.util.ArrayList;
@@ -28,6 +32,16 @@ public final class GermlineDenoisingModelArgumentCollection implements Serializa
     public static final String ENABLE_BIAS_FACTORS_LONG_NAME = "enable-bias-factors";
     public static final String ACTIVE_CLASS_PADDING_HYBRID_MODE_LONG_NAME = "active-class-padding-hybrid-mode";
 
+    // these model parameters will be extracted from provided model in CASE mode
+    private static final List<String> HIDDEN_ARGS_CASE_MODE = ImmutableList.of(
+            MAX_BIAS_FACTORS_LONG_NAME,
+            INTERVAL_PSI_SCALE_LONG_NAME,
+            LOG_MEAN_BIAS_STANDARD_DEVIATION_LONG_NAME,
+            INIT_ARD_REL_UNEXPLAINED_VARIANCE_LONG_NAME,
+            ENABLE_BIAS_FACTORS_LONG_NAME,
+            NUM_GC_BINS_LONG_NAME,
+            GC_CURVE_STANDARD_DEVIATION_LONG_NAME);
+
     public enum CopyNumberPosteriorExpectationMode {
         MAP("map"),
         EXACT("exact"),
@@ -168,7 +182,11 @@ public List<String> generatePythonArguments(final GermlineCNVCaller.RunMode runM
         return arguments;
     }
 
-    public void validate() {
+    public void validate(final CommandLineArgumentParser clpParser, final GermlineCNVCaller.RunMode runMode) {
+        if (runMode == GermlineCNVCaller.RunMode.CASE)
+            HIDDEN_ARGS_CASE_MODE.forEach(a -> Utils.validateArg(
+                    !clpParser.getNamedArgumentDefinitionByAlias(a).getHasBeenSet(),
+                    String.format("Argument '--%s' cannot be set in the CASE mode.", a)));
         ParamUtils.isPositive(maxBiasFactors,
                 String.format("Maximum number of bias factors (%s) must be positive.",
                         MAX_BIAS_FACTORS_LONG_NAME));

src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java

@@ -5,6 +5,7 @@
 import org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection;
 import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
 import org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument;
+import org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection;
 import org.broadinstitute.hellbender.utils.IntervalMergingRule;
 import org.testng.annotations.Test;
 
@@ -71,6 +72,22 @@ public void testCaseWithoutModel() {
         runCommandLine(argsBuilder);
     }
 
+    @Test(groups = {"python"}, expectedExceptions = IllegalArgumentException.class)
+    public void testCaseWithHiddenArguments() {
+        final ArgumentsBuilder argsBuilder = new ArgumentsBuilder();
+        Arrays.stream(TEST_COUNT_FILES, 0, 5).forEach(argsBuilder::addInput);
+        argsBuilder.add(GermlineCNVCaller.RUN_MODE_LONG_NAME, GermlineCNVCaller.RunMode.CASE.name())
+                .add(GermlineCNVCaller.CONTIG_PLOIDY_CALLS_DIRECTORY_LONG_NAME,
+                        CONTIG_PLOIDY_CALLS_OUTPUT_DIR.getAbsolutePath())
+                .add(CopyNumberStandardArgument.MODEL_LONG_NAME,
+                        new File(OUTPUT_DIR, "test-germline-cnv-cohort-model").getAbsolutePath())
+                .add(StandardArgumentDefinitions.OUTPUT_LONG_NAME, OUTPUT_DIR.getAbsolutePath())
+                .add(CopyNumberStandardArgument.OUTPUT_PREFIX_LONG_NAME, "test-germline-cnv-case");
+        // add argument that is not applicable in CASE mode
+        argsBuilder.add(GermlineDenoisingModelArgumentCollection.INTERVAL_PSI_SCALE_LONG_NAME, 0.1);
+        runCommandLine(argsBuilder);
+    }
+
     @Test(groups = {"python"}, enabled = false)
     public void testCohortWithInputModel() {
     }