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Merge pull request #118 from broadinstitute/ami-typoInCoveredByNSamplesSites 

fix typos in argument docs in CoveredByNSamplesSites and rewrite an unac...
This commit is contained in:
Eric Banks 2013-03-18 11:10:10 -07:00
parent 2b80068164 0e9c1913ff
commit a36e2b8f9d
1 changed files with 4 additions and 7 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java
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@ -81,10 +81,10 @@ public class CoveredByNSamplesSites extends RodWalker<GenomeLoc, Integer> 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<GenomeLoc, Integer> implem
Collection<VariantContext> 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<GenomeLoc, Integer> 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");
}