gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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
..
datasources GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
downsampling Make downsampler classes themselves generic (instead of just the Downsampler interface) 2012-06-13 16:43:39 -04:00
executive Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
filters GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
iterators Removing extended event related unit tests 2012-04-02 14:40:36 -04:00
refdata Bugfixes and testdata cleanup 2012-05-24 13:26:05 -04:00
report GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
samples Added function to get founders IDs in SampleDB 2012-04-25 12:49:36 -04:00
traversals First pass of the asynchronous block loader. 2011-11-18 15:02:59 -05:00
walkers Algorithmically faster version of DiffEngine 2012-06-14 16:42:30 -04:00
EngineFeaturesIntegrationTest.java More extensive testing of type of error thrown in multi-threaded walker test 2012-04-13 09:23:33 -04:00
GenomeAnalysisEngineUnitTest.java Allow processing of empty intervals, but warn user when this case is encountered. 2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant. 2011-08-10 12:20:18 -04:00