diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java index bff2ace63..92034da70 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java @@ -81,10 +81,10 @@ public class CoveredByNSamplesSites extends RodWalker implem @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); - @Argument(fullName = "minCoverage", shortName = "minCov",doc = "only samples that have covarage bigger then minCoverage will be counted",required = false) + @Argument(fullName = "minCoverage", shortName = "minCov",doc = "only samples that have coverage bigger than minCoverage will be counted",required = false) int minCoverage = 10; - @Argument(fullName = "precentageOfSamples", shortName = "percentage", doc = "only sites where at list percentageOfSamples of the samples have good coverage, will be emited", required = false) + @Argument(fullName = "percentageOfSamples", shortName = "percentage", doc = "only sites where at least percentageOfSamples of the samples have good coverage, will be emitted", required = false) double percentageOfSamples = 0.9; @Override @@ -95,8 +95,6 @@ public class CoveredByNSamplesSites extends RodWalker implem Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation()); if ( VCs.size() == 0 ) return null; - if(VCs.size() != 1) - throw new RuntimeException("there are more then one vc: "+VCs.size()); boolean emitSite = false; for(VariantContext vc : VCs){ @@ -135,12 +133,11 @@ public class CoveredByNSamplesSites extends RodWalker implem } /** - * Tell the user the number of sites processed and how many passed. Close out the new intervals file. * - * @param result pair of *the number of sites seen and number of sites passed the filter. + * @param result the number of sites that passed the filter. */ public void onTraversalDone(Integer result) { - logger.info(result+" sites that have "+(percentageOfSamples*100)+"% of the samples with at list "+minCoverage+" coverage.\n"); + logger.info(result+" sites that have "+(percentageOfSamples*100)+"% of the samples with at least "+minCoverage+" coverage.\n"); }