From d925f76edc8492b4c59d4755dd8dcef4b6981f92 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Mon, 16 May 2011 13:35:51 +0000 Subject: [PATCH] Cutting down on the number of info lines in VQSR so that I can read the warning messages git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5810 348d0f76-0448-11de-a6fe-93d51630548a --- .../variantrecalibration/VariantRecalibratorEngine.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java index e87048a13..da92ab98b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java @@ -68,10 +68,11 @@ public class VariantRecalibratorEngine { model.maximizationStep( data ); currentChangeInMixtureCoefficients = model.normalizePMixtureLog10(); model.expectationStep(data); - logger.info("Current change in mixture coefficients = " + String.format("%.5f", currentChangeInMixtureCoefficients)); - logger.info("Finished iteration " + iteration ); + if( iteration % 5 == 0 ) { // cut down on the number of output lines so that users can read the warning messages + logger.info("Finished iteration " + iteration + ". \tCurrent change in mixture coefficients = " + String.format("%.5f", currentChangeInMixtureCoefficients)); + } if( iteration > 2 && currentChangeInMixtureCoefficients < MIN_PROB_CONVERGENCE ) { - logger.info("Convergence!"); + logger.info("Convergence after " + iteration + " iterations!"); break; } }