Added an argument mode manager and a demonstration of how it might be used in HaplotypeCaller --dragen-mode

src/main/java/org/broadinstitute/hellbender/cmdline/ModeArgumentUtils.java

@@ -0,0 +1,115 @@
+package org.broadinstitute.hellbender.cmdline;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.broadinstitute.barclay.argparser.CommandLineArgumentParser;
+import org.broadinstitute.barclay.argparser.CommandLineParser;
+import org.broadinstitute.barclay.argparser.NamedArgumentDefinition;
+import org.broadinstitute.hellbender.exceptions.GATKException;
+
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
+import java.util.*;
+
+/**
+ * This class is a static helper for implementing 'mode arguments' by tools. A mode argument is defined as
+ * an argument which controls the setting of multiple (other) arguments to preset values, thereby resulting
+ * in the tool being used in a specific 'mode'. In this sense, a mode is simply a macro of sorts. A mode
+ * argument might be binary (in which case the associated argument and their values will be set when it is true)
+ * or be an enum (in which case a different set of arguments and value be set according to the selected value).
+ *
+ * The detection of the mode (i.e. the implementation of the mode argument) is the tool's responsibility. Following
+ * that, a public method of this class, setArgValues, can be used to install the associated argument values
+ * in the command parser, which will propagate them into the associate tools instance fields.
+ *
+ * The setting of the arguments is done such that argument already specified on the command line are not
+ * overwritten. This allows for mode refinement - i.e. the setting of the mode while turing some of its arguments
+ * to specific values.
+ *
+ * NOTE: This utility relies on the argument engine having already been executed. Consequently, the best place in the
+ *       standard GATKTool would be in the #customCommandLineArgumentValidation() or at a similar stage since that gets
+ *       executed after Barclay parsing is complete but before the tool has done anything with the filled arguments.
+ */
+
+public final class ModeArgumentUtils {
+
+    protected static final Logger logger = LogManager.getLogger(ModeArgumentUtils.class);
+
+    /**
+     * Set a group of  arguments (and associated fields) to the specified values - thereby implementing a mode
+     *
+     * The method does not overwrite arguments already set on the command line (as indicated by the parser)
+     * Additionally, the method emits a warning message indicating which argument were set by the mode and
+     * to which values.
+     *
+     * NOTE: This does not validate that the specified mode was actually set, that responsibility is left to tool authors.
+     *
+     * @param parser - commandline parser associated with the tool. This should be an instance of CommandLineArgumentParser
+     * @param argValues - an array of arguments and values to potentially set. The order of elements in the array
+     *                  is arg0,value0,arg1,value1 ...
+     * @param modeName - the name of the mode being set. This is used in textual message, such as the warning
+     *                 issued to notify the user of the changed argument and not for validation that the argument was set.
+     */
+    public static void setArgValues(final CommandLineParser parser, final String[] argValues, final String modeName) {
+        final Map<String, String>  modifiedArgs = new LinkedHashMap<>();
+
+        for ( int i = 0 ; i < argValues.length ; i += 2 ) {
+            if ( !hasBeenSet(parser, argValues[i]) ) {
+                String parserMessage = setValue(parser, argValues[i], argValues[i+1]);
+
+                if ( StringUtils.isEmpty(parserMessage) ) {
+                    modifiedArgs.put(argValues[i], argValues[i + 1]);
+                } else {
+                    modifiedArgs.put(argValues[i], argValues[i + 1] + " (" + parserMessage + ")");
+                }
+            } else {
+                logger.info("parameter not set by the '" + modeName + "' argument mode, as it was already set on the command line: " + argValues[i]);
+            }
+        }
+
+        logModeNotice(modifiedArgs, modeName);
+    }
+
+    private static boolean hasBeenSet(final CommandLineParser parser, final String alias) {
+
+        if ( parser instanceof CommandLineArgumentParser ) {
+            NamedArgumentDefinition namedArg = ((CommandLineArgumentParser)parser).getNamedArgumentDefinitionByAlias(alias);
+
+            return (namedArg != null) ? namedArg.getHasBeenSet() : false;
+        } else {
+            throw new IllegalArgumentException("command line parser is not CommandLineArgumentParser");
+        }
+    }
+
+    private static String setValue(final CommandLineParser parser, final String alias, final String value) {
+        if ( parser instanceof CommandLineArgumentParser ) {
+            NamedArgumentDefinition namedArg = ((CommandLineArgumentParser)parser).getNamedArgumentDefinitionByAlias(alias);
+            if ( namedArg == null ) {
+                throw new IllegalArgumentException("alias not found: " + alias);
+            }
+
+            PrintStream         ps = new PrintStream(new ByteArrayOutputStream());
+            List<String>        values = Arrays.asList(value);
+            namedArg.setArgumentValues((CommandLineArgumentParser)parser, ps, values);
+            return ps.toString();
+        } else {
+            throw new IllegalArgumentException("command line parser is not CommandLineArgumentParser");
+        }
+    }
+
+    private static void logModeNotice(final Map<String, String> modifiedArgs, final String modeName) {
+        logger.warn("*************************************************************************");
+        logger.warn(String.format("* %-69s *", "--" + modeName + " was enabled"));
+        logger.warn("* The following arguments have had their inputs overwritten:            *");
+        modifiedArgs.forEach((name, value) -> {
+            logger.warn(String.format("* %-69s *", "--" + name + " " + value));
+        });
+        logger.warn("*                                                                       *");
+        logger.warn("* If you would like to run this mode with different inputs for any      *");
+        logger.warn("* of the above arguments please manually construct the command or       *");
+        logger.warn("* add your specific inputs after the mode argument. This mode           *");
+        logger.warn("* will not override inputs explicitly provided.                         *");
+        logger.warn("*************************************************************************");
+    }
+}

src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java

@@ -21,12 +21,14 @@ public final class GenotypeCalculationArgumentCollection implements Serializable
     public static final String MAX_GENOTYPE_COUNT_LONG_NAME = "max-genotype-count";
     public static final String SAMPLE_PLOIDY_SHORT_NAME = "ploidy";
     public static final String SAMPLE_PLOIDY_LONG_NAME = "sample-ploidy";
+    public static final String GENOTYPE_ASSIGNMENT_METHOD_LONG_NAME = "genotype-assignment-method";
+    public static final String USE_POSTERIORS_TO_CALCULATE_QUAL_LONG_NAME = "use-posteriors-to-calculate-qual";
 
     public static final double DEFAULT_STANDARD_CONFIDENCE_FOR_CALLING = 30.0;
     public static final int DEFAULT_MAX_ALTERNATE_ALLELES = 6;
     public static final int DEFAULT_MAX_GENOTYPE_COUNT = 1024;
 
-    @Argument(fullName="use-posteriors-to-calculate-qual", shortName="gp-qual", optional = true, doc = "if available, use the genotype posterior probabilities to calculate the site QUAL")
+    @Argument(fullName= USE_POSTERIORS_TO_CALCULATE_QUAL_LONG_NAME, shortName="gp-qual", optional = true, doc = "if available, use the genotype posterior probabilities to calculate the site QUAL")
     public boolean usePosteriorProbabilitiesToCalculateQual = false;
 
     /**
@@ -188,6 +190,6 @@ public GenotypeCalculationArgumentCollection clone() {
     @Argument(fullName= NUM_REF_SAMPLES_LONG_NAME,doc="Number of hom-ref genotypes to infer at sites not present in a panel",optional=true)
     public int numRefIfMissing = 0;
 
-    @Argument(fullName= "genotype-assignment-method", shortName = "gam", doc = "How we assign genotypes", optional = true)
+    @Argument(fullName= GENOTYPE_ASSIGNMENT_METHOD_LONG_NAME, shortName = "gam", doc = "How we assign genotypes", optional = true)
     public GenotypeAssignmentMethod genotypeAssignmentMethod = GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN;
 }

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java

@@ -53,6 +53,7 @@ public abstract class AssemblyBasedCallerArgumentCollection {
     private static final SWParameters DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS = SmithWatermanAlignmentConstants.NEW_SW_PARAMETERS;
     /** See documentation at {@link SmithWatermanAlignmentConstants#ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS}. */
     private static final SWParameters DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS = SmithWatermanAlignmentConstants.ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS;
+    public static final String SOFT_CLIP_LOW_QUALITY_ENDS_LONG_NAME = "soft-clip-low-quality-ends";
 
     public ReadThreadingAssembler createReadThreadingAssembler() {
         final ReadThreadingAssembler assemblyEngine = assemblerArgs.makeReadThreadingAssembler();
@@ -161,7 +162,7 @@ public ReadThreadingAssembler createReadThreadingAssembler() {
     public boolean forceCallFiltered = false;
 
     @Advanced
-    @Argument(fullName = "soft-clip-low-quality-ends", doc = "If enabled will preserve low-quality read ends as softclips (used for DRAGEN-GATK BQD genotyper model)", optional = true)
+    @Argument(fullName = SOFT_CLIP_LOW_QUALITY_ENDS_LONG_NAME, doc = "If enabled will preserve low-quality read ends as softclips (used for DRAGEN-GATK BQD genotyper model)", optional = true)
     public boolean softClipLowQualityEnds = false;
 
     @Advanced

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCaller.java

@@ -7,6 +7,7 @@
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor;
+import org.broadinstitute.hellbender.cmdline.ModeArgumentUtils;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.cmdline.argumentcollections.ReferenceInputArgumentCollection;
 import org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup;
@@ -160,14 +161,18 @@ public List<ReadFilter> getDefaultReadFilters() {
     }
 
     /**
-     * This is being used to set the mapping quality filter when in dragen mode... there are problems here...
+     * This is being used to set the mapping quality filter when in dragen mode. This is also where make alterations to the input arguments based on DragenMode.
      */
     protected String[] customCommandLineValidation() {
         if (hcArgs.dragenMode) {
             final GATKReadFilterPluginDescriptor readFilterPlugin =
                     getCommandLineParser().getPluginDescriptor(GATKReadFilterPluginDescriptor.class);
             Optional<ReadFilter> filterOptional = readFilterPlugin.getResolvedInstances().stream().filter(rf -> rf instanceof MappingQualityReadFilter).findFirst();
             filterOptional.ifPresent(readFilter -> ((MappingQualityReadFilter) readFilter).minMappingQualityScore = 1);
+            ModeArgumentUtils.setArgValues(
+                    getCommandLineParser(),
+                    hcArgs.getDragenNameValuePairs(),
+                    HaplotypeCallerArgumentCollection.DRAGEN_GATK_MODE_LONG_NAME);
         }
         return null;
     }
@@ -216,44 +221,6 @@ public void onTraversalStart() {
             logger.warn("*************************************************************************");
         }
 
-        if (hcArgs.dragenMode) {
-            logger.warn("*************************************************************************");
-            logger.warn("* DRAGEN-GATK mode enabled                                              *");
-            logger.warn("* The following arguments have had their inputs overwritten:            *");
-            logger.warn("* --apply-frd                                                           *");
-            logger.warn("* --apply-bqd                                                           *");
-            logger.warn("* --transform-dragen-mapping-quality                                    *");
-            logger.warn("* --soft-clip-low-quality-ends                                          *");
-            logger.warn("* --mapping-quality-threshold-for-genotyping  1                         *");
-            logger.warn("* --minimum-mapping-quality  1                                          *");
-            logger.warn("* --allele-informative-reads-overlap-margin  1                          *");
-            logger.warn("* --disable-cap-base-qualities-to-map-quality                           *");
-            logger.warn("* --enable-dynamic-read-disqualification-for-genotyping                 *");
-            logger.warn("* --expected-mismatch-rate-for-read-disqualification  0.03              *");
-            logger.warn("* --genotype-assignment-method USE_POSTERIOR_PROBABILITIES              *");
-            logger.warn("* --padding-around-indels  150                                          *");
-            logger.warn("* --standard-min-confidence-threshold-for-calling 3.0                   *");
-            logger.warn("* --use-posteriors-to-calculate-qual                                    *");
-            logger.warn("* --allele-informative-reads-overlap-margin  1                          *");
-            logger.warn("*                                                                       *");
-            logger.warn("* If you would like to run DRAGEN-GATK with different inputs for any    *");
-            logger.warn("* of the above arguments please manually construct the command.         *");
-            logger.warn("*************************************************************************");
-            hcArgs.applyBQD = true;
-            hcArgs.applyFRD = true;
-            hcArgs.transformDRAGENMapQ = true;
-            hcArgs.softClipLowQualityEnds = true;
-            hcArgs.mappingQualityThreshold = 1;
-            hcArgs.informativeReadOverlapMargin = 1;
-            hcArgs.likelihoodArgs.disableCapReadQualitiesToMapQ = true;
-            hcArgs.likelihoodArgs.enableDynamicReadDisqualification = true;
-            hcArgs.likelihoodArgs.expectedErrorRatePerBase = 0.03;
-            hcArgs.standardArgs.genotypeArgs.genotypeAssignmentMethod = GenotypeAssignmentMethod.USE_POSTERIOR_PROBABILITIES;
-            hcArgs.standardArgs.genotypeArgs.standardConfidenceForCalling = 3.0;
-            hcArgs.standardArgs.genotypeArgs.usePosteriorProbabilitiesToCalculateQual = true;
-            assemblyRegionArgs.indelPaddingForGenotyping = 150;
-        }
-
         final VariantAnnotatorEngine variantAnnotatorEngine = new VariantAnnotatorEngine(makeVariantAnnotations(),
                 hcArgs.dbsnp.dbsnp, hcArgs.comps,  hcArgs.emitReferenceConfidence != ReferenceConfidenceMode.NONE, false);
         hcEngine = new HaplotypeCallerEngine(hcArgs, assemblyRegionArgs, createOutputBamIndex, createOutputBamMD5, getHeaderForReads(), getReferenceReader(referenceArguments), variantAnnotatorEngine);