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Bug fixes and misc. improvements to running the adaptive context tools 

-- Better output file name defaults
-- Fixed nasty bug where I included non-existant quals in the contexts to process because they showed up in the Cycle covariate
-- Data is processed in qual order now, so it's easier to see progress
-- Logger messages explaining where we are in the process
-- When in UPDATE mode we still write out the information for an equivalent prune by depth for post analysis
This commit is contained in:
Mark DePristo 2012-08-03 17:53:46 -04:00
parent afa70a13a9
commit b4841548f1
1 changed files with 2 additions and 1 deletions
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3
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
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@ -324,7 +324,8 @@ public class RecalDatumNode<T extends RecalDatum> {
while ( root.size() > maxElements ) {
// remove the lowest penalty element, and continue
root = root.removeLowestPenaltyNode();
logger.debug("pruneByPenalty root size is now " + root.size() + " of max " + maxElements);
if ( logger.isDebugEnabled() )
logger.debug("pruneByPenalty root size is now " + root.size() + " of max " + maxElements);
}
// our size is below the target, so we are good, return