Pulling out common caller arguments into its own StandardCallerArgumentCollection base class so that every caller isn't exposed to the unused arguments from every other caller.

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
 import com.google.java.contract.Ensures;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
 import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.commandline.*;
@@ -189,7 +190,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     protected String[] annotationClassesToUse = { "Standard" };
 
     @ArgumentCollection
-    private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
+    private StandardCallerArgumentCollection SCAC = new StandardCallerArgumentCollection();
 
     // the calculation arguments
     private UnifiedGenotyperEngine UG_engine = null;
@@ -240,7 +241,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
         samplesList.addAll( samples );
         // initialize the UnifiedGenotyper Engine which is used to call into the exact model
-        UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP; // the GLmodel isn't used by the HaplotypeCaller but it is dangerous to let the user change this argument
+        final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection( SCAC ); // this adapter is used so that the full set of unused UG arguments aren't exposed to the HC user
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC.clone(), logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
         UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY; // low values used for isActive determination only, default/user-specified values used for actual calling
         UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY; // low values used for isActive determination only, default/user-specified values used for actual calling

public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java

@@ -0,0 +1,62 @@
+package org.broadinstitute.sting.gatk.arguments;
+
+import org.broadinstitute.sting.commandline.Advanced;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
+import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: rpoplin
+ * Date: 8/20/12
+ * A collection of arguments that are common to the various callers.
+ * This is pulled out so that every caller isn't exposed to the arguments from every other caller.
+ */
+
+public class StandardCallerArgumentCollection {
+    /**
+     * The expected heterozygosity value used to compute prior likelihoods for any locus. The default priors are:
+     * het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2
+     */
+    @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false)
+    public Double heterozygosity = UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY;
+
+    @Argument(fullName = "genotyping_mode", shortName = "gt_mode", doc = "Specifies how to determine the alternate alleles to use for genotyping", required = false)
+    public GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY;
+
+    @Argument(fullName = "output_mode", shortName = "out_mode", doc = "Specifies which type of calls we should output", required = false)
+    public UnifiedGenotyperEngine.OUTPUT_MODE OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY;
+
+    /**
+     * The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with
+     * confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this
+     * is the default).
+     */
+    @Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false)
+    public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0;
+
+    /**
+     * This argument allows you to emit low quality calls as filtered records.
+     */
+    @Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)", required = false)
+    public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0;
+
+    /**
+     * When the UnifiedGenotyper is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding
+     */
+    @Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES", required=false)
+    public RodBinding<VariantContext> alleles;
+
+    /**
+     * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES),
+     * then only this many alleles will be used.  Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it
+     * scales exponentially based on the number of alternate alleles.  Unless there is a good reason to change the default value, we highly recommend
+     * that you not play around with this parameter.
+     */
+    @Advanced
+    @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
+    public int MAX_ALTERNATE_ALLELES = 3;
+}

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

@@ -26,11 +26,12 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 
-public class UnifiedArgumentCollection {
+public class UnifiedArgumentCollection extends StandardCallerArgumentCollection {
 
     @Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- SNP is the default option, while INDEL is also available for calling indels and BOTH is available for calling both together", required = false)
     public GenotypeLikelihoodsCalculationModel.Model GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP;
@@ -42,13 +43,6 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false)
     protected AlleleFrequencyCalculationModel.Model AFmodel = AlleleFrequencyCalculationModel.Model.EXACT;
 
-    /**
-     * The expected heterozygosity value used to compute prior likelihoods for any locus. The default priors are:
-     * het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2
-     */
-    @Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false)
-    public Double heterozygosity = UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY;
-
     /**
      * The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily
      * distinguish between PCR errors vs. sequencing errors.  The practical implication for this value is that it
@@ -57,26 +51,6 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "pcr_error_rate", shortName = "pcr_error", doc = "The PCR error rate to be used for computing fragment-based likelihoods", required = false)
     public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE;
 
-    @Argument(fullName = "genotyping_mode", shortName = "gt_mode", doc = "Specifies how to determine the alternate alleles to use for genotyping", required = false)
-    public GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY;
-
-    @Argument(fullName = "output_mode", shortName = "out_mode", doc = "Specifies which type of calls we should output", required = false)
-    public UnifiedGenotyperEngine.OUTPUT_MODE OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY;
-
-    /**
-     * The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with
-     * confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this
-     * is the default).
-     */
-    @Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false)
-    public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0;
-
-    /**
-     * This argument allows you to emit low quality calls as filtered records.
-     */
-    @Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)", required = false)
-    public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0;
-
     /**
      * Note that calculating the SLOD increases the runtime by an appreciable amount.
      */
@@ -90,12 +64,6 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "annotateNDA", shortName = "nda", doc = "If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site", required = false)
     public boolean ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = false;
 
-    /**
-     * When the UnifiedGenotyper is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding
-     */
-    @Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES", required=false)
-    public RodBinding<VariantContext> alleles;
-
     /**
      * The minimum confidence needed in a given base for it to be used in variant calling.  Note that the base quality of a base
      * is capped by the mapping quality so that bases on reads with low mapping quality may get filtered out depending on this value.
@@ -107,16 +75,6 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false)
     public Double MAX_DELETION_FRACTION = 0.05;
 
-    /**
-     * If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES),
-     * then only this many alleles will be used.  Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it
-     * scales exponentially based on the number of alternate alleles.  Unless there is a good reason to change the default value, we highly recommend
-     * that you not play around with this parameter.
-     */
-    @Advanced
-    @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
-    public int MAX_ALTERNATE_ALLELES = 3;
-
     @Hidden
     @Argument(fullName = "cap_max_alternate_alleles_for_indels", shortName = "capMaxAltAllelesForIndels", doc = "Cap the maximum number of alternate alleles to genotype for indel calls at 2; overrides the --max_alternate_alleles argument; GSA production use only", required = false)
     public boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = false;
@@ -139,7 +97,6 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "min_indel_fraction_per_sample", shortName = "minIndelFrac", doc = "Minimum fraction of all reads at a locus that must contain an indel (of any allele) for that sample to contribute to the indel count for alleles", required = false)
     public double MIN_INDEL_FRACTION_PER_SAMPLE = 0.25;
 
-
     /**
      * This argument informs the prior probability of having an indel at a site.
      */
@@ -274,5 +231,16 @@ public class UnifiedArgumentCollection {
         return uac;
     }
 
+    public UnifiedArgumentCollection() { }
 
+    public UnifiedArgumentCollection( final StandardCallerArgumentCollection SCAC ) {
+        super();
+        this.alleles = SCAC.alleles;
+        this.GenotypingMode = SCAC.GenotypingMode;
+        this.heterozygosity = SCAC.heterozygosity;
+        this.MAX_ALTERNATE_ALLELES = SCAC.MAX_ALTERNATE_ALLELES;
+        this.OutputMode = SCAC.OutputMode;
+        this.STANDARD_CONFIDENCE_FOR_CALLING = SCAC.STANDARD_CONFIDENCE_FOR_CALLING;
+        this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING;
+    }
 }