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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
This commit is contained in:
rpoplin 2011-05-16 13:35:51 +00:00
parent 5a7444e186
commit d925f76edc
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
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@ -68,10 +68,11 @@ public class VariantRecalibratorEngine {
model.maximizationStep( data ); model.maximizationStep( data );
currentChangeInMixtureCoefficients = model.normalizePMixtureLog10(); currentChangeInMixtureCoefficients = model.normalizePMixtureLog10();
model.expectationStep(data); model.expectationStep(data);
logger.info("Current change in mixture coefficients = " + String.format("%.5f", currentChangeInMixtureCoefficients)); 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 ); logger.info("Finished iteration " + iteration + ". \tCurrent change in mixture coefficients = " + String.format("%.5f", currentChangeInMixtureCoefficients));
}
if( iteration > 2 && currentChangeInMixtureCoefficients < MIN_PROB_CONVERGENCE ) { if( iteration > 2 && currentChangeInMixtureCoefficients < MIN_PROB_CONVERGENCE ) {
logger.info("Convergence!"); logger.info("Convergence after " + iteration + " iterations!");
break; break;
} }
} }