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Make it more clear what is going on with the by-hapmap validation status in the dbSNP rod 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4289 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-09-15 17:29:31 +00:00
parent 0a06fbdb94
commit b5d2e299d2
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
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@ -145,6 +145,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
logger.info("Found input variant track with name " + d.getName());
} else if ( d.getName().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
logger.info("Found dbSNP track for use in training with weight = " + WEIGHT_DBSNP);
logger.info("\tsites in dbSNP track tagged with by-hapmap validation status will be used in training with weight = " + WEIGHT_HAPMAP);
foundDBSNP = true;
} else if ( d.getName().equals("hapmap") ) {
logger.info("Found HapMap track for use in training with weight = " + WEIGHT_HAPMAP);
@ -230,12 +231,12 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
public void onTraversalDone( ExpandingArrayList<VariantDatum> reduceSum ) {
logger.info( "There are " + reduceSum.size() + " variants with > 0 clustering weight and qual > threshold (--qualThreshold = " + QUAL_THRESHOLD + ")" );
logger.info( "The annotations used for clustering are: " + annotationKeys );
final VariantDataManager dataManager = new VariantDataManager( reduceSum, annotationKeys );
reduceSum.clear(); // Don't need this ever again, clean up some memory
logger.info( "There are " + dataManager.numVariants + " variants with > 0 clustering weight and qual > threshold (--qualThreshold = " + QUAL_THRESHOLD + ")" );
logger.info( "The annotations used for clustering are: " + annotationKeys );
dataManager.normalizeData(); // Each data point is now [ (x - mean) / standard deviation ]
// Create either the Gaussian Mixture Model or the Nearest Neighbors model and run it