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misc cleanup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5893 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-05-27 16:49:20 +00:00
parent 9e834391fe
commit 2227f49220
1 changed files with 15 additions and 17 deletions
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32
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -208,29 +208,27 @@ public class VariantDataManager {
private static double decodeAnnotation( final String annotationKey, final VariantContext vc, final boolean jitter ) {
double value;
if( annotationKey.equals("QUAL") ) {
value = vc.getPhredScaledQual();
} else {
try {
try {
if( annotationKey.equals("QUAL") ) {
value = vc.getPhredScaledQual();
} else {
value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
if (Double.isInfinite(value))
value = Double.NaN;
else
if( jitter && ( annotationKey.equalsIgnoreCase("HRUN") || annotationKey.equalsIgnoreCase("FS") ) ) { // Integer valued annotations must be jittered a bit to work in this GMM
value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
}
if(annotationKey.equals("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
} catch( final Exception e ) {
value = Double.NaN; // The VQSR works with missing data now by marginalizing over the missing dimension when evaluating clusters.
if( !warnedUserMissingValue ) {
logger.warn("WARNING: Missing value detected for " + annotationKey + ". The VQSR will work with missing data by marginalizing over this dimension for this variant. This warning message is only shown once so there may be other annotations missing as well.");
warnedUserMissingValue = true;
if( Double.isInfinite(value) ) { value = Double.NaN; }
if( jitter && ( annotationKey.equalsIgnoreCase("HRUN") || annotationKey.equalsIgnoreCase("FS") ) ) { // Integer valued annotations must be jittered a bit to work in this GMM
value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
}
if( annotationKey.equals("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
}
} catch( final Exception e ) {
value = Double.NaN; // The VQSR works with missing data now by marginalizing over the missing dimension when evaluating clusters.
if( !warnedUserMissingValue ) {
logger.warn("WARNING: Missing value detected for " + annotationKey + ". The VQSR will work with missing data by marginalizing over this dimension for this variant. This warning message is only shown once so there may be other annotations missing as well.");
warnedUserMissingValue = true;
}
}
return value;
}