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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
This commit is contained in:
rpoplin 2010-02-10 15:52:20 +00:00
parent 6652b992f7
commit 0b1e243a7b
4 changed files with 22 additions and 16 deletions
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25
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -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 {
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()) );
standardClassNames.add( covClass.getName() );
}
Collections.sort(standardClassNames); // Sort the list of class names
for( String className : standardClassNames ) {
for( Class<?> covClass : standardClasses ) { // Find the class that matches this class name
if( covClass.getName().equals( className ) ) {
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()) );
}
}
}
}
}

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -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)

1
java/src/org/broadinstitute/sting/utils/PackageUtils.java
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@ -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;

10
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
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@ -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" +
" -cov QualityScoreCovariate" +
" -cov CycleCovariate" +
" -cov DinucCovariate" +
" -standard" +
" -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" +
" -cov QualityScoreCovariate" +
" -cov CycleCovariate" +
" -cov DinucCovariate" +
" -standard" +
" --solid_recal_mode SET_Q_ZERO" +
" -recalFile %s",
1, // just one output file