CountCovariates now sorts the list of standard covariate classes coming from PackageUtils.getClassesImplementingInterface(). As a result some of the integration tests now make use of -standard

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2817 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java

@@ -165,14 +165,25 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
         }
         // Next add the standard covariates if -standard was specified by the user
         if( USE_STANDARD_COVARIATES ) {
+            // We want the standard covariates to appear in a consistent order but the packageUtils method gives a random order
+            // A list of Classes can't be sorted, but a list of Class names can be
+            final List<String> standardClassNames = new ArrayList<String>();
             for( Class<?> covClass : standardClasses ) {
-                try {
+                standardClassNames.add( covClass.getName() );
-                    final Covariate covariate = (Covariate)covClass.newInstance();
+            }
-                    requestedCovariates.add( covariate );
+            Collections.sort(standardClassNames); // Sort the list of class names
-                } catch ( InstantiationException e ) {
+            for( String className : standardClassNames ) {
-                    throw new StingException( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
+                for( Class<?> covClass : standardClasses ) { // Find the class that matches this class name
-                } catch ( IllegalAccessException e ) {
+                    if( covClass.getName().equals( className ) ) {
-                    throw new StingException( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
+                        try {
+                            final Covariate covariate = (Covariate)covClass.newInstance();
+                            requestedCovariates.add( covariate );
+                        } catch ( InstantiationException e ) {
+                            throw new StingException( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
+                        } catch ( IllegalAccessException e ) {
+                            throw new StingException( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
+                        }
+                    }
                 }
             }
         }

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -38,7 +38,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     @Argument(shortName="printVariants", doc="If true, prints the variants in all of the variant tracks that are examined", required=false)
     public boolean printVariants = false;
 
-    @Argument(shortName="badHWEThreshold", doc="Only sites with deviations froim Hardy-Weinberg equilibrium with P-values < than this threshold are flagged", required=false)
+    @Argument(shortName="badHWEThreshold", doc="Only sites with deviations from Hardy-Weinberg equilibrium with P-values < than this threshold are flagged", required=false)
     public double badHWEThreshold = 1e-3;
 
     @Argument(fullName="evalContainsGenotypes", shortName = "G", doc="If true, the input list of variants will be treated as a genotyping file, containing assertions of actual genotype values for a particular person.  Analyses that only make sense on at the population level will be disabled, while those operating on genotypes will be enabled", required=false)

java/src/org/broadinstitute/sting/utils/PackageUtils.java

@@ -5,6 +5,7 @@ import org.reflections.scanners.SubTypesScanner;
 import org.reflections.util.AbstractConfiguration;
 import org.reflections.util.ClasspathHelper;
 
+import java.util.Collections;
 import java.util.Set;
 import java.util.ArrayList;
 import java.util.List;

java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java

@@ -123,10 +123,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                             " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
                             " -T CountCovariates" +
                             " -I " + bam +
-                            " -cov ReadGroupCovariate" +
+                            " -standard" +
-                            " -cov QualityScoreCovariate" +
-                            " -cov CycleCovariate" +
-                            " -cov DinucCovariate" +
                             " -U" +
                             " -L 1:10,000,000-20,000,000" +
                             " --solid_recal_mode REMOVE_REF_BIAS" +
@@ -184,10 +181,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -L 1:10,000,000-10,200,000" +
-                            " -cov ReadGroupCovariate" +
+                            " -standard" +
-                            " -cov QualityScoreCovariate" +
-                            " -cov CycleCovariate" +
-                            " -cov DinucCovariate" +
                             " --solid_recal_mode SET_Q_ZERO" +
                             " -recalFile %s",
                     1, // just one output file