From 119d449b46657f0e7e24fb39a1c1b35e40358eed Mon Sep 17 00:00:00 2001 From: chartl Date: Tue, 23 Feb 2010 20:43:15 +0000 Subject: [PATCH] Formatting changes git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2877 348d0f76-0448-11de-a6fe-93d51630548a --- .../oneoffprojects/walkers/CoverageStatistics.java | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java index 87a53084a..cd3d12e70 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java @@ -38,18 +38,18 @@ public class CoverageStatistics extends LocusWalker, DepthOf @Argument(fullName = "start", doc = "Starting (left endpoint) for granular binning", required = false) int start = 1; @Argument(fullName = "stop", doc = "Ending (right endpoint) for granular binning", required = false) - int stop = 500; + int stop = 1000; @Argument(fullName = "nBins", doc = "Number of bins to use for granular binning", required = false) int nBins = 20; @Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to 50.", required = false) byte minMappingQuality = 50; @Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth. Defaults to 20.", required = false) byte minBaseQuality = 20; - @Argument(fullName = "perLocusStatisticsFile", shortName = "locusFile", doc = "File to output per-locus statistics to; if unprovided these will not be calculated") + @Argument(fullName = "perLocusStatisticsFile", shortName = "locusFile", doc = "File to output per-locus statistics to; if unprovided these will not be calculated", required = false) File perLocusStatisticsFile = null; - @Argument(fullName = "perSampleStatisticsFile", shortName = "sampleFile", doc = "File to output per-sample statistics to; if unprovided will go to standard (-o) output") + @Argument(fullName = "perSampleStatisticsFile", shortName = "sampleFile", doc = "File to output per-sample statistics to; if unprovided will go to standard (-o) output", required = false) File perSampleStatisticsFile = null; - @Argument(fullName = "summaryStatisticsFile", shortName = "summaryFile", doc = "File to output summary (mean, median) statistics to; if unprovided will go to standard (-o) output") + @Argument(fullName = "summaryStatisticsFile", shortName = "summaryFile", doc = "File to output summary (mean, median) statistics to; if unprovided will go to standard (-o) output", required = false) File summaryStatisticsFile = null; //////////////////////////////////////////////////////////////////////////////////// @@ -258,6 +258,8 @@ class DepthOfCoverageStats { binLeftEndpoints[b] = leftEnd; } + binLeftEndpoints[binLeftEndpoints.length-1] = upper; + return binLeftEndpoints; } @@ -269,6 +271,7 @@ class DepthOfCoverageStats { this.binLeftEndpoints = leftEndpoints; granularHistogramBySample = new HashMap(); meanCoverages = new HashMap(); + meanCoverages.put(DepthOfCoverageStats.ALL_SAMPLES,0.0); nLoci = 0; totalDepth = 0; }