gatk3的最后一个经典版本3.8

kshakir 2ef66af903 Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high. ... Moved the BamListWriter from FCP to ListWriterFunction in the Queue core. Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s. Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-28 23:33:58 +00:00
R	Updating a few graphical parameters and making sure everything fits together	2011-01-28 18:44:23 +00:00
analysis/depristo/distributedGATK	Documentation and cleanup of the distributed GATK implementation. Detailed documentation -- given that Matt will be extending the system in the near future -- about how the locking and processing trackers work. Added error trapping to note that distributed, shared-memory parallelism isn't yet implemented, instead of just not working silently. General utility function for the analysis of distributedGATK operation in the analysis directory	2011-01-28 03:40:09 +00:00
archive	Moving GLF code to archive	2011-01-15 22:42:42 +00:00
c	Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.	2010-12-17 14:49:15 +00:00
doc	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
java	Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.	2011-01-28 23:33:58 +00:00
lua	A script to convert an intervals file into a sorted unoverlapping intervals file. Super fast implementation using multiple hashes, should do the job instantly no matter how big the intervals are.	2011-01-28 21:46:41 +00:00
matlab	Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function	2009-11-30 20:02:25 +00:00
packages	Adding the native jna support libraries from the jna.jar to the Queue package jar.	2011-01-08 10:48:30 +00:00
perl	Fixed bug that required users to use the recordOriginalLocation option	2011-01-05 23:12:14 +00:00
python	updated to work with the new tearsheet	2011-01-28 18:46:38 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.	2011-01-28 23:33:58 +00:00
settings	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
shell	V3 of the distributed GATK. High-efficiency implementation. Support for status tracking for debugging and display. Still not safe for production use due to NFS filelock problem. V4 will use alternative file locking mechanism	2011-01-24 16:45:07 +00:00
testdata	VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary	2010-11-15 22:19:22 +00:00
LICENSE	Adding a license to the root directory in case BOSC checks for one. Has the	2010-04-20 16:04:29 +00:00
build.xml	FASTQ directory is gone	2011-01-13 15:16:06 +00:00
ivy.xml	Adding lucene dependency for file locking -- may be removed in the near future	2011-01-24 18:59:42 +00:00