From b4841548f12086e8928d4c749bf66fa29f2eaf4f Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 3 Aug 2012 17:53:46 -0400 Subject: [PATCH] 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 --- .../sting/utils/recalibration/RecalDatumNode.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java index 1409af7d0..e6ec6a520 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -324,7 +324,8 @@ public class RecalDatumNode { 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