From 5e2677063401c98c45ef2759b186ac93406976b8 Mon Sep 17 00:00:00 2001 From: hanna Date: Thu, 9 Jul 2009 17:26:59 +0000 Subject: [PATCH] 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 --- .../sting/gatk/executive/MicroScheduler.java | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java index 63834177a..b67ecb87f 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java @@ -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); }