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Bug fixes for Andrey 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@930 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-06-07 18:19:51 +00:00
parent b48508a226
commit 98396732ba
2 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -77,7 +77,7 @@ public class GenomeAnalysisEngine {
if (argCollection.HAPMAPChipFile != null)
bindConvenienceRods("hapmap-chip", "GFF", argCollection.HAPMAPChipFile);
if ( argCollection.intervals != null )
bindConvenienceRods("interval", "Intervals", argCollection.intervals);
bindConvenienceRods("interval", "Intervals", argCollection.intervals.replaceAll(",", ""));
// parse out the rod bindings
ReferenceOrderedData.parseBindings(logger, argCollection.RODBindings, rods);

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java
View File

@ -26,8 +26,8 @@ public class VariantCounter extends BasicVariantAnalysis {
List<String> s = new ArrayList<String>();
s.add(String.format("n bases covered: %d", nBasesCovered));
s.add(String.format("sites: %d", nSNPs));
s.add(String.format("variant rate: %.5f confident variants per base", nSNPs / (1.0 * nBasesCovered)));
s.add(String.format("variant rate: 1 / %d confident variants per base", nBasesCovered / nSNPs));
s.add(String.format("variant rate: %.5f confident variants per base", nSNPs / (1.0 * Math.max(nBasesCovered, 1))));
s.add(String.format("variant rate: 1 / %d confident variants per base", nBasesCovered / Math.max(nSNPs, 1)));
return s;
}
}