Mark DePristo 9de8077eeb Working (efficient?) implementation of NanoScheduler ... -- Groups inputs for each thread so that we don't have one thread execution per map() call -- Added shutdown function -- Documentation everywhere -- Code cleanup -- Extensive unittests -- At this point I'm ready to integrate it into the engine for CPU parallel read walkers		2012-08-24 15:34:23 -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	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
gatk	Spotted a potential bug where sample IDs passed in from the meta data were only checked against the sample IDs in the VCF header if the input file happened to be a meta data file rather than a fam file. Added a check for fam files as well, and added an integration test to cover each case.	2012-08-23 11:43:19 -07:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Working (efficient?) implementation of NanoScheduler	2012-08-24 15:34:23 -04:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -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	On the way to really sorting out HMS error handling	2012-07-25 22:11:10 -04:00