03e1713988
Better support for specifying read filters to apply directly from the walkers.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1212 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 23:59:53 +00:00
aa17c4a468
Farewell, functionalj. You promised much, but you could not deliver.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@847 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 01:35:49 +00:00
01a3cb27c7
@Required / @Allows flags for main arguments.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@751 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 23:26:17 +00:00
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
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
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
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
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
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
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
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
hanna
depristo
aaron