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Clearer logger output when not using by-hapmap 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4308 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-09-18 16:10:42 +00:00
parent 7e58d8ed61
commit c6351a11d6
2 changed files with 6 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
View File

@ -139,7 +139,9 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
logger.info("Found input variant track with name " + d.getName());
} else if ( d.getName().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
logger.info("Found dbSNP track for use in training with weight = " + WEIGHT_DBSNP);
logger.info("\tsites in dbSNP track tagged with by-hapmap validation status will be used in training with weight = " + WEIGHT_HAPMAP);
if( !NO_BY_HAPMAP_VALIDATION_STATUS ) {
logger.info("\tsites in dbSNP track tagged with by-hapmap validation status will be used in training with weight = " + WEIGHT_HAPMAP);
}
foundDBSNP = true;
} else if ( d.getName().equals("hapmap") ) {
logger.info("Found HapMap track for use in training with weight = " + WEIGHT_HAPMAP);

4
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -159,7 +159,9 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
logger.info("Found input variant track with name " + d.getName());
} else if ( d.getName().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
logger.info("Found dbSNP track with prior probability = Q" + PRIOR_DBSNP);
logger.info("\tsites in dbSNP track tagged with by-hapmap validation status will be given prior probability = Q" + PRIOR_HAPMAP);
if( !NO_BY_HAPMAP_VALIDATION_STATUS ) {
logger.info("\tsites in dbSNP track tagged with by-hapmap validation status will be given prior probability = Q" + PRIOR_HAPMAP);
}
foundDBSNP = true;
} else if ( d.getName().equals("hapmap") ) {
logger.info("Found HapMap track with prior probability = Q" + PRIOR_HAPMAP);