Guillermo del Angel 5a9a37ba01 Pool caller improvements: a) Log ref sample depth at every called site (will add more ref-related annotations later), b) Make -glm POOLBOTH work in case we want to genotype snp's and indels together, c) indel bug fix (pool and non-pool): prevent a bad GenomeLoc to be formed if we're running GGA and incoming alleles are larger than ref window size (typically 400 bb)		2012-06-29 11:08:16 -04:00
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R	Bugfix for R 2.15 not including reshape	2012-06-14 16:42:29 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Pool caller improvements: a) Log ref sample depth at every called site (will add more ref-related annotations later), b) Make -glm POOLBOTH work in case we want to genotype snp's and indels together, c) indel bug fix (pool and non-pool): prevent a bad GenomeLoc to be formed if we're running GGA and incoming alleles are larger than ref window size (typically 400 bb)	2012-06-29 11:08:16 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Temporary fake release directories for Bamboo testing purposes	2012-05-31 16:04:07 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Merged bug fix from Stable into Unstable	2012-06-26 14:55:41 -04:00
testdata	Moved most testdata from public to private	2012-06-21 15:17:19 -04:00