Mark DePristo 45603f58cd Refactoring and unit testing GenomeLocParser ... -- Moved previously inner class to MRUCachingSAMSequenceDictionary, and unit test to 100% coverage -- Fully document all functions in GenomeLocParser -- Unit tests for things like parsePosition (shocking it wasn't tested!) -- Removed function to specifically create GenomeLocs for VariantContexts. The fact that you must incorporate END attributes in the context means that createGenomeLoc(Feature) works correctly -- Depreciated (and moved functionality) of setStart, setStop, and incPos to GenomeLoc -- Unit test coverage at like 80%, moving to 100% with next commit		2013-01-30 09:47:47 -05:00
..
R	Fix a nasty bug in reading GATK reports with a single line	2012-09-10 20:14:13 -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	Refactoring and unit testing GenomeLocParser	2013-01-30 09:47:47 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Remove the ability to package GATK/Queue Lite from the build system	2013-01-28 02:42:37 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Making metrics a required parameter in MarkDuplicates	2013-01-25 17:49:49 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00