From dad9bb11920b0877e6bd31cbede5f030a62d1d62 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 30 Jul 2012 15:46:00 -0400 Subject: [PATCH] Changes order of writing BaseRecalibrator results so that if R blows up you still get a meaningful tree --- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index e95a0e6c1..ddd75e232 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -275,13 +275,16 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed public void onTraversalDone(Long result) { logger.info("Calculating quantized quality scores..."); quantizeQualityScores(); + + logger.info("Writing recalibration report..."); + generateReport(); + logger.info("...done!"); + if (!RAC.NO_PLOTS) { logger.info("Generating recalibration plots..."); generatePlots(); } - logger.info("Writing recalibration report..."); - generateReport(); - logger.info("...done!"); + logger.info("Processed: " + result + " sites"); }