Mauricio Carneiro fce5cb9f35 Few category changes		2012-07-25 17:23:02 -04:00
..
arguments	Make -qq arg hidden for now since it's still very experimental	2012-07-18 15:43:25 -04:00
contexts	Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.	2012-06-15 15:55:03 -04:00
datasources	Catch 'too many open files' errors that show up when trying to read the bam index. All that needs to be done is to flesh out the original error message (because it will get caught later and rethrown correctly).	2012-07-18 12:57:34 -04:00
downsampling	Make downsampler classes themselves generic (instead of just the Downsampler interface)	2012-06-13 16:43:39 -04:00
examples	As promised in the release notes for 1.6, I am removing the old deprecated genotyping framework revolving around the misordering of alleles and have moved the fixed version in its place in preparation for release 1.7 (or 2.0?).	2012-05-01 16:18:24 -04:00
executive	Context covariate optimizations were not suited for multiple threads, so I removed them (since that ended up being much, much easier than trying to make the covariates thread local). Added -nt 2 layer to BQSR integration tests to confirm that it now works with multiple threads.	2012-07-25 13:38:07 -04:00
filters	Updating Read Filter documentation	2012-07-25 15:05:47 -04:00
io	BCF2 cleanup	2012-06-26 15:28:33 -04:00
iterators	Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.	2012-06-15 15:55:03 -04:00
phonehome	Put RunReport S3 upload on timeout thread	2012-07-17 12:19:39 -04:00
refdata	BCF2 cleanup	2012-06-26 15:28:33 -04:00
report	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
resourcemanagement	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
samples	Added function to get founders IDs in SampleDB	2012-04-25 12:49:36 -04:00
traversals	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
walkers	Few category changes	2012-07-25 17:23:02 -04:00
CommandLineExecutable.java	Old -B syntax is long gone at this point. Safe to remove the warning.	2012-04-02 22:25:16 -04:00
CommandLineGATK.java	Few category changes	2012-07-25 17:23:02 -04:00
DownsampleType.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
DownsamplingMethod.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenomeAnalysisEngine.java	Register GATK-full-only walkers and rethrow the missing walker error as a not supported in GATK lite error	2012-07-25 14:11:03 -04:00
ReadMetrics.java	Counts of records failing filters are displayed sorted	2011-10-06 18:42:26 -07:00
ReadProperties.java	Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.	2012-06-15 15:55:03 -04:00
WalkerManager.java	Removed support for walkers ending with "Walker" from the engine.	2012-07-20 17:27:11 -04:00
package-info.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00