Mark DePristo 63a9ae817a Ensure thread-safety of CachingIndexedFastaSequenceFile ... -- Cosmetic cleanup of ReadReferenceView -- TraverseReadsNano provides the reference context, since it's thread-safe -- Cleanup CachingIndexedFastaSequenceFile. Add docs, remove unnecessary setters -- Expand CachingIndexedFastaSequenceFileUnitTest to test explicitly multi-threaded safety.		2012-08-27 12:11:54 -04:00
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R	Fix for missing formatter in R 2.15	2012-08-17 11:49:02 -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	Ensure thread-safety of CachingIndexedFastaSequenceFile	2012-08-27 12:11:54 -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