Christopher Hartl 79ef3325bd Fix a NullPointerException that could occur in DoC if the user requested an interval summary but never provided a -L argument. This situation is now checked for and a UserError thrown instead. Also (after a great struggle) pushing some old VR3 code into the central repository which had been improperly pushed (e.g. with rsync rather than git push) into my repository on the server, and never migrated to unstable. In addition, minor convenience function added to the GATKReport that allows an entire row to be added, and a walker that parses out annotations from a tool called VariantEffectPredictor and summarizes annotations across transcripts, and consensus annotations.		2012-06-19 07:50:13 -04:00
..
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	…
doc	…
java	Fix a NullPointerException that could occur in DoC if the user requested an interval summary but never provided a -L argument. This situation is now checked for and a UserError thrown instead. Also (after a great struggle) pushing some old VR3 code into the central repository which had been improperly pushed (e.g. with rsync rather than git push) into my repository on the server, and never migrated to unstable. In addition, minor convenience function added to the GATKReport that allows an entire row to be added, and a walker that parses out annotations from a tool called VariantEffectPredictor and summarizes annotations across transcripts, and consensus annotations.	2012-06-19 07:50:13 -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	MD5DB for integrationtest management now writes out a md5mismatches files for clean analysis	2012-06-14 16:42:27 -04:00
testdata	More testdata test files	2012-06-14 16:42:35 -04:00