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Formatting changes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2877 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-02-23 20:43:15 +00:00
parent 173956927b
commit 119d449b46
1 changed files with 7 additions and 4 deletions
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11
java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java
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@ -38,18 +38,18 @@ public class CoverageStatistics extends LocusWalker<Map<String,Integer>, DepthOf
@Argument(fullName = "start", doc = "Starting (left endpoint) for granular binning", required = false) @Argument(fullName = "start", doc = "Starting (left endpoint) for granular binning", required = false)
int start = 1; int start = 1;
@Argument(fullName = "stop", doc = "Ending (right endpoint) for granular binning", required = false) @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) @Argument(fullName = "nBins", doc = "Number of bins to use for granular binning", required = false)
int nBins = 20; int nBins = 20;
@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to 50.", required = false) @Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to 50.", required = false)
byte minMappingQuality = 50; byte minMappingQuality = 50;
@Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth. Defaults to 20.", required = false) @Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth. Defaults to 20.", required = false)
byte minBaseQuality = 20; 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; 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; 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; File summaryStatisticsFile = null;
//////////////////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////////////////////
@ -258,6 +258,8 @@ class DepthOfCoverageStats {
binLeftEndpoints[b] = leftEnd; binLeftEndpoints[b] = leftEnd;
} }
binLeftEndpoints[binLeftEndpoints.length-1] = upper;
return binLeftEndpoints; return binLeftEndpoints;
} }
@ -269,6 +271,7 @@ class DepthOfCoverageStats {
this.binLeftEndpoints = leftEndpoints; this.binLeftEndpoints = leftEndpoints;
granularHistogramBySample = new HashMap<String,int[]>(); granularHistogramBySample = new HashMap<String,int[]>();
meanCoverages = new HashMap<String,Double>(); meanCoverages = new HashMap<String,Double>();
meanCoverages.put(DepthOfCoverageStats.ALL_SAMPLES,0.0);
nLoci = 0; nLoci = 0;
totalDepth = 0; totalDepth = 0;
} }