delangel ef47a69c50 a) First fully functional (sort of) version of walker that parses Beagle imputation output files and produce a vcf with imputed genotypes. ... More doc/info to follow shortly. Issues still to be solved: a) Walker changes all genotypes based on Beagle data, but annotations on the original VCF are unchanged. They should in theory be recomputed based on new genotypes. b) Current implementation is ugly, dirty unwieldy and will necessitate a refactoring soon so I can keep my pride. Most aesthetically affronting issue right now is that we read the full Beagle files at initialization and keep them in memory, but a more delicate implementation would just read from files on a marker by marker basis. Issue that currently prevents this is that BufferedReader() instances don't seem to play nice when called from the map() function. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3488 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-04 20:37:25 +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	a) First fully functional (sort of) version of walker that parses Beagle imputation output files and produce a vcf with imputed genotypes.	2010-06-04 20:37:25 +00:00
test/org/broadinstitute/sting	updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function.	2010-06-04 06:34:26 +00:00