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incorporated comments from review, made variables final, made AF paramater hidden, and added bounds checking to AF value

This commit is contained in:
Kristian Cibulskis 2014-04-16 19:29:25 -04:00
parent 7115cadbd8
commit 6b9e38c8bb
1 changed files with 8 additions and 2 deletions
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10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java
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@ -127,6 +127,7 @@ public class SimulateReadsForVariants extends RodWalker<Integer, Integer> {
/**
* Use this argument to simulate events at a non-50/50 allele fraction represented in the VCF by AF (used for somatic event simulation)
*/
@Hidden
@Argument(fullName="useAFAsAlleleFraction", shortName="AF", doc="Use AF in VCF as event allele fraction ", required=false)
public boolean useAFAsAlleleFraction = false;
/**
@ -296,14 +297,19 @@ public class SimulateReadsForVariants extends RodWalker<Integer, Integer> {
* @param ref the original reference context
* @param useAFAsAlleleFraction use AF tag to indicate allele fraction
*/
private void generateReadsForVariant(final VariantContext vc, final ReferenceContext ref, boolean useAFAsAlleleFraction) {
private void generateReadsForVariant(final VariantContext vc, final ReferenceContext ref, final boolean useAFAsAlleleFraction) {
final int refLength = vc.getReference().getBases().length;
final ArtificialHaplotype refHap = constructHaplotype(vc.getReference(), refLength, ref);
final ArtificialHaplotype altHap = constructHaplotype(vc.getAlternateAllele(0), refLength, ref);
final double refAlleleFraction = (useAFAsAlleleFraction)?1-vc.getAttributeAsDouble(VCFConstants.ALLELE_FREQUENCY_KEY, 0.5):0.5;
if (refAlleleFraction < 0.0 || refAlleleFraction > 1.0 || Double.isNaN(refAlleleFraction) || Double.isInfinite(refAlleleFraction) ) {
throw new UserException.MalformedVCF("Error in AF, must be between 0 and 1 but was " + refAlleleFraction);
}
int gi = 0;
double refAlleleFraction = (useAFAsAlleleFraction)?1-vc.getAttributeAsDouble(VCFConstants.ALLELE_FREQUENCY_KEY, 0.5):0.5f;
for ( final Genotype g : vc.getGenotypes() ) {
final int myDepth = sampleDepth();
for ( int d = 0; d < myDepth; d++ ) {