Eric Banks ac0c44720b I started to put together a set of unit tests for the PileupElement creation functionality of LocusIteratorByState and found pretty quickly that it's definitely still busted for indels. The data provider is nowhere near comprehensive yet, but I need to sit back and think about how to really test some of the functionality of LIBS. Committing what I have for now because at the very least it'll be helpful going forward (failing tests are commented out with TODO).		2012-08-30 22:49:13 -04:00
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R	Actually load the library necessary to compactPDF	2012-08-28 08:06:47 -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	I started to put together a set of unit tests for the PileupElement creation functionality of LocusIteratorByState and found pretty quickly that it's definitely still busted for indels. The data provider is nowhere near comprehensive yet, but I need to sit back and think about how to really test some of the functionality of LIBS. Committing what I have for now because at the very least it'll be helpful going forward (failing tests are commented out with TODO).	2012-08-30 22:49:13 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
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	One less Queue command line requirement: -tempDir now defaults to .queue/tmp.	2012-08-27 12:04:50 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00