zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Adding User Exception to VQSR for the case of trying to cluster with an annotation that doesn't exist in the input VCF 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5816 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-05-18 19:47:51 +00:00
parent 218354e338
commit 4b00fd2688
1 changed files with 8 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
View File

@ -50,10 +50,14 @@ public class VariantDataManager {
public void normalizeData() {
boolean foundZeroVarianceAnnotation = false;
for( int iii = 0; iii < meanVector.length; iii++ ) { //BUGBUG: to clean up
final double theMean = mean(iii); //BUGBUG: to clean up
final double theSTD = standardDeviation(theMean, iii); //BUGBUG: to clean up
for( int iii = 0; iii < meanVector.length; iii++ ) {
final double theMean = mean(iii);
final double theSTD = standardDeviation(theMean, iii);
logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
if( Double.isNaN(theMean) ) {
throw new UserException.BadInput("Annotations values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator");
}
foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);
if( annotationKeys.get(iii).toLowerCase().contains("ranksum") ) { // BUGBUG: to clean up
for( final VariantDatum datum : data ) {
@ -216,7 +220,7 @@ public class VariantDataManager {
} 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 but there may be other annotations missing as well.");
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;
}
}