gatk-3.8/public/java/test/org/broadinstitute/sting
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
..
alignment Reinitialize random seed in the bwa bindings from the fixed seed stored in the 2011-07-22 13:41:53 -04:00
commandline Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -04:00
gatk Algorithmically faster version of DiffEngine 2012-06-14 16:42:30 -04:00
jna Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. 2012-05-29 11:18:22 -04:00
utils Initial version of clean, fast formatting routines built dynamically from a VCF header 2012-06-14 16:42:30 -04:00
BaseTest.java Initial version of clean, fast formatting routines built dynamically from a VCF header 2012-06-14 16:42:30 -04:00
MD5DB.java Algorithmically faster version of DiffEngine 2012-06-14 16:42:30 -04:00
MD5Mismatch.java Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
StingTextReporter.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
WalkerTest.java Initial version of clean, fast formatting routines built dynamically from a VCF header 2012-06-14 16:42:30 -04:00