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Bug fix for variant optimizer. Remember to close the PrintStreams it uses to output the cluster files. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3046 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-03-19 15:07:32 +00:00
parent bb7e0c27fd
commit cdec84aa8f
5 changed files with 19 additions and 9 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/ApplyVariantClustersWalker.java
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@ -56,7 +56,7 @@ public class ApplyVariantClustersWalker extends RodWalker<ExpandingArrayList<Var
///////////////////////////// /////////////////////////////
// Command Line Arguments // Command Line Arguments
///////////////////////////// /////////////////////////////
@Argument(fullName="target_titv", shortName="titv", doc="The target Ti/Tv ratio towards which to optimize. (~~2.2 for whole genome experiments)", required=true) @Argument(fullName="target_titv", shortName="titv", doc="The target Ti/Tv ratio towards which to optimize. (~~2.1 for whole genome experiments)", required=true)
private double TARGET_TITV = 2.1; private double TARGET_TITV = 2.1;
@Argument(fullName="desired_num_variants", shortName="dV", doc="The desired number of variants to keep in a theoretically filtered set", required=false) @Argument(fullName="desired_num_variants", shortName="dV", doc="The desired number of variants to keep in a theoretically filtered set", required=false)
private int DESIRED_NUM_VARIANTS = 0; private int DESIRED_NUM_VARIANTS = 0;

8
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java
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@ -47,10 +47,15 @@ public class VariantDataManager {
public VariantDataManager( final ExpandingArrayList<VariantDatum> dataList, final ExpandingArrayList<String> _annotationKeys ) { public VariantDataManager( final ExpandingArrayList<VariantDatum> dataList, final ExpandingArrayList<String> _annotationKeys ) {
numVariants = dataList.size(); numVariants = dataList.size();
data = dataList.toArray( new VariantDatum[numVariants]); data = dataList.toArray( new VariantDatum[numVariants] );
if( numVariants <= 0 ) { if( numVariants <= 0 ) {
throw new StingException( "There are zero variants! (or possibly a problem with integer overflow)" ); throw new StingException( "There are zero variants! (or possibly a problem with integer overflow)" );
} }
if( _annotationKeys == null ) {
numAnnotations = 0;
meanVector = null;
varianceVector = null;
} else {
numAnnotations = _annotationKeys.size() + 1; // +1 for QUAL numAnnotations = _annotationKeys.size() + 1; // +1 for QUAL
if( numAnnotations <= 0 ) { if( numAnnotations <= 0 ) {
throw new StingException( "There are zero annotations! (or possibly a problem with integer overflow)" ); throw new StingException( "There are zero annotations! (or possibly a problem with integer overflow)" );
@ -58,6 +63,7 @@ public class VariantDataManager {
meanVector = new double[numAnnotations]; meanVector = new double[numAnnotations];
varianceVector = new double[numAnnotations]; varianceVector = new double[numAnnotations];
isNormalized = false; isNormalized = false;
}
annotationKeys = _annotationKeys; annotationKeys = _annotationKeys;
} }

1
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDatum.java
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@ -35,5 +35,6 @@ public class VariantDatum {
public double[] annotations; public double[] annotations;
public boolean isTransition; public boolean isTransition;
public boolean isKnown; public boolean isKnown;
public boolean isTrueVariant;
public double qual; public double qual;
} }

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java
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@ -282,6 +282,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
outputFile.println(-1); outputFile.println(-1);
} }
} }
outputFile.close();
} catch (Exception e) { } catch (Exception e) {
e.printStackTrace(); e.printStackTrace();
System.exit(-1); System.exit(-1);
@ -384,6 +385,8 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
( numKnownTi ==0 || numKnownTv == 0 ? "NaN" : ( ((double)numKnownTi) / ((double)numKnownTv) ) ) + "," + ( numKnownTi ==0 || numKnownTv == 0 ? "NaN" : ( ((double)numKnownTi) / ((double)numKnownTv) ) ) + "," +
( numNovelTi ==0 || numNovelTv == 0 ? "NaN" : ( ((double)numNovelTi) / ((double)numNovelTv) ))); ( numNovelTi ==0 || numNovelTv == 0 ? "NaN" : ( ((double)numNovelTi) / ((double)numNovelTv) )));
} }
outputFile.close();
} }

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizer.java
View File

@ -51,7 +51,7 @@ public class VariantOptimizer extends RodWalker<ExpandingArrayList<VariantDatum>
///////////////////////////// /////////////////////////////
// Command Line Arguments // Command Line Arguments
///////////////////////////// /////////////////////////////
@Argument(fullName="target_titv", shortName="titv", doc="The target Ti/Tv ratio towards which to optimize. (~~2.2 for whole genome experiments)", required=true) @Argument(fullName="target_titv", shortName="titv", doc="The target Ti/Tv ratio towards which to optimize. (~~2.1 for whole genome experiments)", required=true)
private double TARGET_TITV = 2.1; private double TARGET_TITV = 2.1;
@Argument(fullName="ignore_input_filters", shortName="ignoreFilters", doc="If specified the optimizer will use variants even if the FILTER column is marked in the VCF file", required=false) @Argument(fullName="ignore_input_filters", shortName="ignoreFilters", doc="If specified the optimizer will use variants even if the FILTER column is marked in the VCF file", required=false)
private boolean IGNORE_INPUT_FILTERS = false; private boolean IGNORE_INPUT_FILTERS = false;