A cleaner interface: now everyone can use UG's initialize method

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1860 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -85,13 +85,27 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<GenotypeCall>, Genot
     /**
      * Initialize the samples, output, and genotype calculation model
      *
-     * *** OTHER WALKERS SHOULD NOT CALL THIS METHOD.  USE initializePublic() INSTEAD! ***
-     * 
      **/
     public void initialize() {
 
-        initializePublic();
+        // get all of the unique sample names
+        samples = new HashSet<String>();
+        List<SAMReadGroupRecord> readGroups = getToolkit().getSAMFileHeader().getReadGroups();
+        for ( SAMReadGroupRecord readGroup : readGroups )
+            samples.add(readGroup.getSample());
 
+        // print them out for debugging (need separate loop to ensure uniqueness)
+        for ( String sample : samples )
+            logger.debug("SAMPLE: " + sample);
+
+        gcm = GenotypeCalculationModelFactory.makeGenotypeCalculation(samples, logger, UAC);
+
+        // *** If we were called by another walker, then we don't ***
+        // *** want to do any of the other initialization steps.  ***
+        if ( VARIANTS_FILE == null && out == null )
+            return;
+
+        // if we got here, then we were instantiated by the GATK engine
         calledByAnotherWalker = false;
 
         // create the output writer stream
@@ -107,25 +121,6 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<GenotypeCall>, Genot
         callsMetrics = new CallMetrics();
     }
 
-    /**
-     * This method should be called by other walkers wanting to use the UnifiedGenotyper.
-     * If the regular initialize() method is called, subsequent calls to map() may result in
-     * exceptions being thrown.
-     */
-    public void initializePublic() {
-        // get all of the unique sample names
-        samples = new HashSet<String>();
-        List<SAMReadGroupRecord> readGroups = getToolkit().getSAMFileHeader().getReadGroups();
-        for ( SAMReadGroupRecord readGroup : readGroups )
-            samples.add(readGroup.getSample());
-
-        // print them out for debugging (need separate loop to ensure uniqueness)
-        for ( String sample : samples )
-            logger.debug("SAMPLE: " + sample);
-
-        gcm = GenotypeCalculationModelFactory.makeGenotypeCalculation(samples, logger, UAC);
-    }
-
     /**
      * Compute at a given locus.
      *

java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java

@@ -41,7 +41,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
 
     public void initialize() {
         ug = new UnifiedGenotyper();
-        ug.initializePublic();
+        ug.initialize();
         refWindow = new ReferenceContextWindow(nPreviousBases);
     }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java

@@ -41,7 +41,7 @@ public class CoverageEvalWalker extends LocusWalker<List<String>, String> {
 
     public void initialize() {
         UG = new UnifiedGenotyper();
-        UG.initializePublic();
+        UG.initialize();
 
         String header = "#Sequence       Position        ReferenceBase   NumberOfReads   MaxMappingQuality       BestGenotype    BtrLod  BtnbLod AA      AC      AG      AT      CC      CG      CT      GG      GT      TT";
         out.println("DownsampledCoverage\tAvailableCoverage\tHapmapChipGenotype\tGenotypeCallType\t"+header.substring(1));

java/src/org/broadinstitute/sting/playground/gatk/walkers/DeNovoSNPWalker.java

@@ -37,7 +37,7 @@ public class DeNovoSNPWalker extends RefWalker<String, Integer>{
 
     public void initialize() {
          UG = new UnifiedGenotyper();
-         UG.initializePublic();
+         UG.initialize();
 
          readGroupSets = getToolkit().getMergedReadGroupsByReaders();
      }

java/src/org/broadinstitute/sting/playground/utils/ArtificialPoolContext.java

@@ -74,7 +74,7 @@ public class ArtificialPoolContext {
     }
 
     public void initializeUG() {
-        ug.initializePublic();
+        ug.initialize();
     }
 
     public void setReadGroupSets(List<Set<String>> rgSets) {