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Changes order of writing BaseRecalibrator results so that if R blows up you still get a meaningful tree

This commit is contained in:
Mark DePristo 2012-07-30 15:46:00 -04:00
parent 0c4e729e13
commit dad9bb1192
1 changed files with 6 additions and 3 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -275,13 +275,16 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> 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");
}