Eric Banks 4bb7a99f08 Given that all classes implementing output stubs already have getters for the underlying OutputStream and File, it makes sense to unify that functionality into the Stub interface. Now it is possible to have an Engine utility method that iterates over all registered stubs to find the one representing a given OutputStream and return the File associated with it.		2012-09-12 11:51:44 -04:00
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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	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	Given that all classes implementing output stubs already have getters for the underlying OutputStream and File, it makes sense to unify that functionality into the Stub interface. Now it is possible to have an Engine utility method that iterates over all registered stubs to find the one representing a given OutputStream and return the File associated with it.	2012-09-12 11:51:44 -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	Update from dbsnp135 to dbsnp137.	2012-08-31 14:06:29 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00