gatk-3.8/public
Mark DePristo 641c6a361e Fix nasty memory leak in new data thread x cpu thread parallelism
-- Basically you cannot safely use instance specific ThreadLocal variables, as these cannot be safely cleaned up.  The old implementation kept pointers to old writers, with huge tribble block indexes, and eventually we crashed out of integration tests
-- See http://weblogs.java.net/blog/jjviana/archive/2010/06/10/threadlocal-thread-pool-bad-idea-or-dealing-apparent-glassfish-memor for more information
-- New implementation uses a borrow/return schedule with a list of N TraversalEngines managed by the MicroScheduler directly.
2012-09-10 20:14:14 -04:00
..
R Fix a nasty bug in reading GATK reports with a single line 2012-09-10 20:14:13 -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 Fix nasty memory leak in new data thread x cpu thread parallelism 2012-09-10 20:14:14 -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 Update from dbsnp135 to dbsnp137. 2012-08-31 14:06:29 -04:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00