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8 Commits (716af47dd5a77ce359fd72676ee7b0d4fff5e678)

Author SHA1 Message Date
jmaguire 716af47dd5 Added NullWalker module (do nothing). 
Added SingleSampleGenotyper module (old-school single sample genotyping).

Added Utils.SortPermutation (return the permutaton that would sort the input array).
Added Utils.PermuteArray (apply a permutation to an array).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@29 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-10 21:26:07 +00:00
hanna ea0a826f8f Clean up 3rd party dependencies. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@27 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-10 19:34:00 +00:00
andrewk e938dbda47 Check for the existence of the module name and return error rather than throwing an exception if not found. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@23 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-04 00:15:35 +00:00
depristo 49a84c965e Added basic GenomeLoc class 
Support for operating on any location in genome (albeit slowly)
Improvements to dbSNP support

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@19 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-02 18:18:48 +00:00
depristo a5c76f7666 Renamed Empty to Count methods in analysisTK 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@15 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-01 23:31:23 +00:00
depristo 0ee2375292 Working on reference ordered data; added build.xml for ant! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@14 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-01 18:27:32 +00:00
depristo f64f3e2d90 Phase II support for generic reference order data set parsing. 
Can read GFF and dbSNP files correctly.  
Traversal engine now supports keeping moving window of reference ordered data along with the locus iterator.
Tested by walking through a sam file keeping track of the dbSNP positions encountered -- they definitely look right...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@13 348d0f76-0448-11de-a6fe-93d51630548a
 2009-02-28 20:47:48 +00:00
depristo 17aabb38f9 Basic reorganization of tree 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@8 348d0f76-0448-11de-a6fe-93d51630548a
 2009-02-28 15:28:56 +00:00