gatk-3.8/public
Mark DePristo 8014178f2f Algorithmically faster version of DiffEngine
-- Now only includes leaf nodes in the summary, i.e., summaries of the form "*.*....*.X", which are really the most valuable to see.  This calculation can be accomplished in linear time for N differences, rather than the previous O(n^2) algorithm
-- Now computes the max number of elements to read correctly.  Counts now the size of the entire element tree, not just the count of the roots, which was painful because the trees vary by orders of magnitude in size.
-- Because of this we can enforce a meaningful, useful value for the max elements in MD5 or 100K, and this works well.
-- Added integration test for new leaf and old pairwise calculations
-- Bugfix for Utils.join(sep, int[]) that was eating the first element of the AD, PL fields
2012-06-14 16:42:30 -04:00
..
R Bugfix for R 2.15 not including reshape 2012-06-14 16:42:29 -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 Algorithmically faster version of DiffEngine 2012-06-14 16:42:30 -04:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Temporary fake release directories for Bamboo testing purposes 2012-05-31 16:04:07 -04:00
perl Update to the bindings for liftOverVCF.pl (to -V from -B) 2011-09-15 15:33:09 -04:00
scala MD5DB for integrationtest management now writes out a md5mismatches files for clean analysis 2012-06-14 16:42:27 -04:00
testdata Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests 2012-05-27 11:17:17 -04:00