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Changed default phasing window size to 10 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4235 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2010-09-08 21:28:36 +00:00
parent 6c27a9bfc6
commit 1b1ec7e52d
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
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@ -67,8 +67,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
@Argument(fullName = "cacheWindowSize", shortName = "cacheWindow", doc = "The window size (in bases) to cache variant sites and their reads; [default:20000]", required = false)
protected Integer cacheWindow = 20000;
@Argument(fullName = "maxPhaseSites", shortName = "maxSites", doc = "The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm; [default:20]", required = false)
protected Integer maxPhaseSites = 20; // 2^20 == 10^6 biallelic haplotypes
@Argument(fullName = "maxPhaseSites", shortName = "maxSites", doc = "The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm; [default:10]", required = false)
protected Integer maxPhaseSites = 10; // 2^10 == 10^3 biallelic haplotypes
@Argument(fullName = "phaseQualityThresh", shortName = "phaseThresh", doc = "The minimum phasing quality score required to output phasing; [default:10.0]", required = false)
protected Double phaseQualityThresh = 10.0; // PQ = 10.0 <=> P(error) = 10^(-10/10) = 0.1, P(correct) = 0.9