zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/java/src/org/broadinstitute/sting/gatk
History
depristo d9588e6083 bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1558 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-09-09 15:36:12 +00:00
..
contexts bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa 2009-09-09 15:36:12 +00:00
datasources LocusIterationByState is now the system deafult. Fixed Aaron's build problem 2009-09-09 01:28:05 +00:00
examples Cleaned division of responsibilities between arguments to map function. Reference has been changed 2009-08-04 21:01:37 +00:00
executive General-purpose management of output streams. 2009-08-23 00:56:02 +00:00
filters Major: allow genotyper to optionally output in 1KG format, including outputting the samples in which indels are found. 2009-07-23 19:53:51 +00:00
io General-purpose management of output streams. 2009-08-23 00:56:02 +00:00
iterators bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa 2009-09-09 15:36:12 +00:00
refdata Lots of changes: (I'll send email out in a sec) 2009-09-07 01:12:09 +00:00
traversals Windowed access to the reference. 2009-08-05 16:29:15 +00:00
walkers bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa 2009-09-09 15:36:12 +00:00
CommandLineExecutable.java General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG 2009-09-04 19:13:37 +00:00
CommandLineGATK.java General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG 2009-09-04 19:13:37 +00:00
GATKArgumentCollection.java Set default value of useLocusIteratorByHanger to FALSE. Otherwise the -LIBH flag is useless and there'd be no wayto "unset" the 'true' value. Old version was (always) using LocusIteratorByHanger. Now default iterator is indeed LocusIteratorByState, and -LIBH will switch back to the old one 2009-09-09 15:09:09 +00:00
GenomeAnalysisEngine.java bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa 2009-09-09 15:36:12 +00:00
Reads.java bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa 2009-09-09 15:36:12 +00:00
WalkerManager.java Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils. 2009-07-21 22:23:28 +00:00
package.html More package-level documentation. 2009-06-17 16:28:45 +00:00