Commit Graph

3 Commits (4fbb6d05d0441e21490a5b0ec032bb8c2200955b)

Author SHA1 Message Date
hanna 4fbb6d05d0 Refactoring. Push the revisions to the common aligner interface down into
the aligner base classes.  Hack the managed implementation to support the
new interface.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 17:08:09 +00:00
hanna 14477bb48e Unidirectional alignments with mismatches now working. Significant refactoring will be required.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1686 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-22 19:05:10 +00:00
hanna c186a49d55 Time for a reorganization. Repackage generally useful alignment classes lower in the package structure, and create a subpackage for bwa-specific code. Repackage BWA alignment code away from BWT representation. Isolate byte- and word-packing streams in another package that will ultimately be killed off en masse.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1648 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-17 23:28:47 +00:00