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8 Commits (40dbc21df75983847e0a55806f9fa8d4fc9c305d)

Author SHA1 Message Date
hanna 2c4de7b5c5 Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along 
the pathway from command line to traversal engine.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@727 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-15 21:02:12 +00:00
hanna e812cfbf55 Refactor common functionality out of WalkerManager and into JVMUtils and PathUtils. Add support for loading walkers from a jar. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@229 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-30 23:20:55 +00:00
depristo 826781a760 The traversal engine now passes the reduce result to OnTraversalDone() in the walker base class 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@210 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-27 13:44:46 +00:00
aaron d115209e86 moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@209 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-27 13:27:04 +00:00
hanna 53fe9acf65 Make command-line arguments available in walker constructor, provide back door from 
walker into GATK itself, do some cleanup of output messages, and add some bug fixes.
Command-line arguments in walkers are now feature-complete, but still a bit messy.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@203 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-26 20:45:27 +00:00
hanna 9e2a373184 Prototype, buggy implementation of walker command-line arguments. Doesn't 
(yet) deal elegantly with even simple cases.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@180 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-25 00:12:00 +00:00
hanna f7363cf935 Support for loading from either a jar or a class directory. Fixes troubles with IntelliJ debugging. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@162 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 03:56:49 +00:00
hanna 63cd1fe201 Push core / playground lower into the tree. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 23:19:54 +00:00