790d2a7776
adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2918 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 15:56:44 +00:00
21d1eba502
Cleaned division of responsibilities between arguments to map function. Reference has been changed
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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
3c40db260d
Added REFERENCE_BASES required annotation for performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1047 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:03:57 +00:00
01a3cb27c7
@Required / @Allows flags for main arguments.
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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
23e9e29964
Changed reads traversals from providing a LocusContext from which the reference sequence
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could be extracted to a char[] containing the reference bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@657 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:45:11 +00:00
7a9cfe1f75
Push reduceInit down a level so that the walker can call into it without weird casts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@638 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 13:46:28 +00:00
f2f9fa3ed4
doc added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@464 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 16:43:25 +00:00
cfee59e0e6
New type hierarchy for Traversals. There's a new package to hold them (traversals) and an easy system to create new ones. We are now one step closer to supporting the execution manager (a totally non-functional version is included here) that actually executes walkers in parallel using N threads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@214 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 15:40:45 +00:00
826781a760
The traversal engine now passes the reduce result to OnTraversalDone() in the walker base class
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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
5f9010116a
Collapse the walker hierarchy, in preparation for in-walker output streams less hokey walker args.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@201 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 16:22:35 +00:00
63cd1fe201
Push core / playground lower into the tree.
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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
aaron
hanna
depristo
asivache