zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
View File

@ -275,13 +275,16 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
public void onTraversalDone(Long result) { public void onTraversalDone(Long result) {
logger.info("Calculating quantized quality scores..."); logger.info("Calculating quantized quality scores...");
quantizeQualityScores(); quantizeQualityScores();
logger.info("Writing recalibration report...");
generateReport();
logger.info("...done!");
if (!RAC.NO_PLOTS) { if (!RAC.NO_PLOTS) {
logger.info("Generating recalibration plots..."); logger.info("Generating recalibration plots...");
generatePlots(); generatePlots();
} }
logger.info("Writing recalibration report...");
generateReport();
logger.info("...done!");
logger.info("Processed: " + result + " sites"); logger.info("Processed: " + result + " sites");
} }