sjia 9b78a789e2 HLA Caller 2.0 Walkers: ... CalculateBaseLikelihoodsWalker.java walks through reads calculates likelihoods using SSG at each base position CalculateAlleleLikelihoodsWalker.java walks through HLA dictionary and calculates likelihoods for allele pairs given output of CalculateBaseLikelihoodsWalker.java CalculatePhaseLikelihoodsWalker.java walks through reads and calculates likelihoods score for allele pairs given phase information File Readers: BaseLikelihoodsFileReader.java reads text file of likelihoods outputted by SSG FrequencyFileReader.java reads text file of HLA allele frequencies PolymorphicSitesFileReader.java reads text file of polymorphic sites in the HLA dictionary SAMFileReader.java reads a sam file (used to read HLA dictionary when in another walker) SimilarityFileReader.java reads a text file of how similar each read is to the closest HLA allele (used to filter misaligned reads) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1744 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-29 20:45:55 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	HLA Caller 2.0 Walkers:	2009-09-29 20:45:55 +00:00
test/org/broadinstitute/sting	Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.	2009-09-28 18:12:32 +00:00