Mark DePristo df90597bfc Performance optimizations and caliper benchmarking code for consolidateCigar ... -- Now that this function is used in the core of LIBS it needed some basic optimizations, which are now complete, pass all unit tests. -- Added caliper benchmark for AlignmentUtils to assess performance (showing new version is 3x-10x faster) -- Remove unused import in ReadStateManager		2013-04-24 11:36:43 -04:00
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R	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -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	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Performance optimizations and caliper benchmarking code for consolidateCigar	2013-04-24 11:36:43 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -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	Small Queue/scala improvements, and commiting pipeline scripts developed for ancient DNA processing for posterity:	2013-04-08 11:52:13 -04:00
testdata	Updating the exampleGRP.grp test file	2013-04-13 09:07:13 -04:00