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Un-reinventing the wheel. --sleep argument removed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2227 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-12-02 20:19:28 +00:00
parent 938017d887
commit dec0a781c2
3 changed files with 0 additions and 33 deletions
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7
java/src/org/broadinstitute/sting/gatk/GATKArgumentCollection.java
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@ -64,10 +64,6 @@ public class GATKArgumentCollection {
@Argument(fullName = "intervals", shortName = "L", doc = "A list of genomic intervals over which to operate. Can be explicitly specified on the command line or in a file.", required = false)
public List<String> intervals = null;
@ElementList(required = false)
@Argument(fullName = "sleep", doc = "If provided, the engine will sleep for this number of milliseconds before starting the analysis -- useful for debugging", required = false)
public long sleep = 0;
@Element(required = false)
@Argument(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
public File referenceFile = null;
@ -223,9 +219,6 @@ public class GATKArgumentCollection {
if (other.walkerArgs.size() != walkerArgs.size()) {
return false;
}
if (other.sleep != sleep) {
return false;
}
for (String s : walkerArgs.keySet()) {
if (!other.walkerArgs.containsKey(s)) {
return false;

8
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -136,14 +136,6 @@ public class GenomeAnalysisEngine {
// save our argument parameter
this.argCollection = args;
if ( args.sleep > 0 ) {
try {
Thread.sleep(args.sleep);
} catch ( InterruptedException e ) {
throw new RuntimeException(e);
}
}
// Prepare the data for traversal.
initializeDataSources(my_walker, filters, argCollection);

18
java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java
View File

@ -33,13 +33,6 @@ public class SecondBaseSkew implements VariantAnnotation {
public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
if ( variation.isSNP() && variation.isBiallelic() ) {
char snp = variation.getAlternativeBaseForSNP();
// try {
// System.out.printf("snp %c, alt is %c%n", snp, getNonref(genotypes, ref.getBase()));
// } catch (IllegalStateException e) {
// System.out.printf("%s is not biallelic%n", variation.toString());
// return null;
// }
Pair<Integer,Double> depthProp = getSecondaryPileupNonrefEstimator(ref.getBase(), pileup, snp);
if ( depthProp == null ) {
return null;
@ -79,21 +72,10 @@ public class SecondBaseSkew implements VariantAnnotation {
}
if ( variantDepth > 0 ) {
//System.out.printf("%d %d %d %d%n", primaryPileup.length, secondaryPileup.length, variantDepth, variantsWithRefSecondBase );
double biasedProportion = ( 1.0 + variantsWithRefSecondBase )/(1.0 + variantDepth );
return new Pair<Integer,Double>(variantDepth+1, biasedProportion);
} else {
return null;
}
}
private char getNonref(List<Genotype> genotypes, char ref) {
for ( Genotype g : genotypes ) {
if ( g.isVariant(ref) ) {
return g.toVariation(ref).getAlternativeBaseForSNP();
}
}
throw new IllegalStateException("List of genotypes did not contain a variant.");
}
}