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Hack the MicroScheduler to be tolerant of RefWalkers. We need to implement a longer-term solution to make it easier for datasources to report problems they've encountered along the way (GSA-103). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1205 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-09 17:26:59 +00:00
parent bc44e08225
commit 5e26770634
1 changed files with 8 additions and 1 deletions
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9
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -212,7 +212,14 @@ public abstract class MicroScheduler {
* @param sum The final reduce output.
*/
protected void printOnTraversalDone(Object sum) {
logger.info(String.format("%n%s",reads.getViolationHistogram()));
// HACK: The microscheduler should be too dumb to know anything about the data
// it's actually processing; it should just funnel anything it receives
// to the traversal engine.
// TODO: Implement code to allow the datasources to print summary info of the
// data they've seen.
if( reads != null && reads.getViolationHistogram().getViolationCount() > 0 )
logger.warn(String.format("%n%s",reads.getViolationHistogram()));
traversalEngine.printOnTraversalDone(sum);
}