delangel 6ecbfa9013 OK, this time REALLY fix cut and paste error ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5880 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-26 19:47:12 +00:00
..
alignment	Fixed Umapped misspelling	2011-02-04 22:21:41 +00:00
analyzecovariates	It was returning 1 when it should return 0	2011-03-31 20:50:38 +00:00
commandline	Removed -debug/--debug_mode.	2011-04-27 10:56:39 +00:00
datasources/pipeline	FCP only adds the expand intervals QFunction once per script instead of once per QFunction using the ExpandTargets scala trait.	2011-02-17 19:09:03 +00:00
gatk	OK, this time REALLY fix cut and paste error	2011-05-26 19:47:12 +00:00
jna	Updated LSF libraries to use Pointer instead of Structure.ByReference for struct arrays since the the latter is autoRead() and LSF doesn't always return null for empty arrays.	2011-03-10 22:58:54 +00:00
oneoffprojects	Now finds the most likely configuration of genotypes given the genotype likelihoods and inheritance constraints. The parental genotypes are now phased as well (the alleles are ordered as A_transmitted|A_untransmitted). Rewrote the way the transmission probability is calculated. This will probably move into core soon.	2011-05-24 01:35:40 +00:00
playground	- No longer prints out non confident calls (they were leading to tables that don't add up and confusing some Pacbio folk).	2011-05-04 19:26:55 +00:00
queue	Somehow checked in a version that was building extensions for everything ("") instead of selected packages. Fixed.	2011-05-16 16:58:37 +00:00
utils	Great! Contracts is working. Fixing some misspecified ones.	2011-05-23 21:00:52 +00:00