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5 Commits (16467ae7cfb32c3e8f01d246ce44c02dde1c9e12)

Author SHA1 Message Date
kiran 16467ae7cf A better (less overflow-y) implementation of multinomialProbability(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@579 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-01 06:28:16 +00:00
kiran b9c9dbb1d7 Added multinomialProbability method. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@545 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-27 15:03:50 +00:00
jmaguire dd408a2a9a First draft of actual pooled EM caller. 
Produces sane looking output on region of 1kG pilot1:

    CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
    CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
    CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
    CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
    CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084

Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@525 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-24 13:42:15 +00:00
kiran 3cda85f2e3 New implementation of binomial probability that accurately computes values down to around 1e-237. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@520 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-24 03:32:04 +00:00
kiran 77e1e9e2f1 Added a static class to house useful math methods. All this has at the moment are methods for comparing doubles and floats, but I suggest that the bulk of our little math methods should be added here to avoid filling up Utils.java with so much random stuff. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@505 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-23 17:45:19 +00:00