From 98396732bae5124284158eba92fa39db126bf4b9 Mon Sep 17 00:00:00 2001 From: depristo Date: Sun, 7 Jun 2009 18:19:51 +0000 Subject: [PATCH] Bug fixes for Andrey git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@930 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 2 +- .../playground/gatk/walkers/varianteval/VariantCounter.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index f385609b4..5c10ad654 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -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); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java index 5bffd4274..9cc18cb15 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java @@ -26,8 +26,8 @@ public class VariantCounter extends BasicVariantAnalysis { List s = new ArrayList(); 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; } } \ No newline at end of file