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9 Commits (2fb45dbd736d39f8b84fb235529af574988d4dbc)

Author SHA1 Message Date
hanna 48713e154c Windowed access to the reference. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1383 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 16:29:15 +00:00
hanna 21d1eba502 Cleaned division of responsibilities between arguments to map function. Reference has been changed 
from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 21:01:37 +00:00
hanna 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
hanna 491ed70b44 TraverseByLocusWindow -- asstd bug fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1109 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 22:51:38 +00:00
hanna ff798fe483 Reintroduce support for interval-based traversals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@749 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-18 22:54:18 +00:00
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 9f5f6f9bc7 N-way parallelism. Works for small test cases. Untested for large test cases. 
-Needs more comprehensive unit testing.
-Needs some basic refactoring.
-Needs rethink of interface boundaries.
-Needs to play more nicely in the /tmp sandbox.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@583 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-01 19:34:09 +00:00
hanna 3af66a462e Make PrintLocusContextWalker less verbose. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@493 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-22 18:28:02 +00:00
hanna e91a429c58 A class to print out as much context about the given locus site as is possible. Useful for testing traversal engines -- run old and new code across a given region and diff the output to make sure they have the same context. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@383 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-13 15:29:55 +00:00