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Zero byte index bug fix for RandomlySplitVariants + cleanup 

-- vcfWriter2 was never being closed in onTraversalDone(), so the on the fly index file was being created but never actually properly written to the file.

-- This bug is ultimately due to the inability of the GATK to allow multiple VCF output writers as @Output arguments, though

-- Removed the unnecessary local variable iFraction, = 1000 * the input fraction argument.  Now the system just uses a double random number and compares to the input fraction at all.  Is there some subtle reason I don't appreciate for this programming construct?
This commit is contained in:
Mark DePristo 2011-11-04 09:45:20 -04:00
parent 5a47c3c8a0
commit 9f260c0dc1
1 changed files with 6 additions and 6 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
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@ -58,15 +58,12 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="fractionToOut1", shortName="fraction", doc="Fraction of records to be placed in out1 (must be 0 >= fraction <= 1); all other records are placed in out2", required=false)
protected double fraction = 0.5;
protected int iFraction;
/**
* Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
*/
public void initialize() {
if ( fraction < 0.0 || fraction > 1.0 )
throw new UserException.BadArgumentValue("fractionToOut1", "this value needs to be a number between 0 and 1");
iFraction = (int)(fraction * 1000.0);
// setup the header info
final List<String> inputNames = Arrays.asList(variantCollection.variants.getName());
@ -93,8 +90,8 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
for ( VariantContext vc : vcs ) {
int random = GenomeAnalysisEngine.getRandomGenerator().nextInt(1000);
if ( random < iFraction )
double random = GenomeAnalysisEngine.getRandomGenerator().nextDouble();
if ( random < fraction )
vcfWriter1.add(vc);
else
vcfWriter2.add(vc);
@ -107,5 +104,8 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
public Integer reduce(Integer value, Integer sum) { return value + sum; }
public void onTraversalDone(Integer result) { logger.info(result + " records processed."); }
public void onTraversalDone(Integer result) {
logger.info(result + " records processed.");
vcfWriter2.close();
}
}