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Minor cleanup

This commit is contained in:
Eric Banks 2011-11-17 12:00:28 -05:00
parent f250b47228
commit e7d41d8d33
1 changed files with 4 additions and 6 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -24,10 +24,8 @@
package org.broadinstitute.sting.gatk.walkers.variantutils; package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.apache.poi.hpsf.Variant;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.text.XReadLines;
@ -275,8 +273,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
private double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 0; private double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 0;
/** /**
* Variants are kept in memory to guarantee that exactly n variants will be chosen randomly, so use it only for a reasonable * Variants are kept in memory to guarantee that exactly n variants will be chosen randomly, so make sure you supply the program with enough memory
* number of variants. Use --select_random_fraction for larger numbers of variants. * given your input set. This option will NOT work well for large callsets; use --select_random_fraction for sets with a large numbers of variants.
*/ */
@Argument(fullName="select_random_number", shortName="number", doc="Selects a number of variants at random from the variant track", required=false) @Argument(fullName="select_random_number", shortName="number", doc="Selects a number of variants at random from the variant track", required=false)
private int numRandom = 0; private int numRandom = 0;
@ -532,7 +530,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
} }
} }
if (SELECT_RANDOM_NUMBER) { if (SELECT_RANDOM_NUMBER) {
randomlyAddVariant(++variantNumber, sub, ref.getBase()); randomlyAddVariant(++variantNumber, sub);
} }
else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) { else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
vcfWriter.add(sub); vcfWriter.add(sub);
@ -705,7 +703,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
return sub; return sub;
} }
private void randomlyAddVariant(int rank, VariantContext vc, byte refBase) { private void randomlyAddVariant(int rank, VariantContext vc) {
if (nVariantsAdded < numRandom) if (nVariantsAdded < numRandom)
variantArray[nVariantsAdded++] = new RandomVariantStructure(vc); variantArray[nVariantsAdded++] = new RandomVariantStructure(vc);