Mark DePristo b3ecfbfce8 Refactor LIBS into component parts, expand unit tests, some code cleanup ... -- Split out all of the inner classes of LIBS into separate independent classes -- Split / add unit tests for many of these components. -- Radically expand unit tests for SAMRecordAlignmentState (the lowest level piece of code) making sure at least some of it works -- No need to change unit tests or integration tests. No change in functionality. -- Added (currently disabled) code to track all submitted reads to LIBS, but this isn't accessible or tested		2013-01-11 15:17:16 -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	Refactor LIBS into component parts, expand unit tests, some code cleanup	2013-01-11 15:17:16 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Remove DepthOfCoverage.java because it is no longer public	2013-01-10 11:45:38 -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	Licensing update -- batch #2	2013-01-11 13:38:11 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00