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#35are ticket numbers.
API change with tests and detailed description of changes.
[API,TEST] Large changes of align module's API. This is a large patch that mostly updates the align module: * The Anchor Gaps specialization is moved from the store module to the align module. * The Array Gaps class is rewritten. * Both Anchor and Array gaps have mostly the same API now, differences are documented. * Greatly unified the interface of the ``globalAlignment()`` and ``localAlignment()`` interface. * The ``LocalAlignmentFinder`` is now called ``LocalAlignmentEnumerator``. * Threw out unused DP algorithms (DP algorithm will be cleaned up in the future, see below). * Clipping of gaps works consistently in both Anchor and Array Gaps data structures. * Wrote a large number of tests for all changes. * Adjusted SeqAn library and apps to new API. All in all, this should make the module more usable, albeit breaking the interface in some cases. There will be a future change by Rene that strongly unifies the DP algorithms. This will not inflict another API change, though, and further simplify the align module.
A fix that solves two tickets:
[FIX-#240,#356] Fixed iteration of ``ModifiedString``s. Quite involved fix that allows iteration of ``ModifiedString`` objects.
A fix that does not have a ticket:
[FIX] Fixed reading of CIGAR string in module bam_io. There was a bug when reading the operation "F", which was translated to FLABBERGASTED. Fixed this to the documented behavior.
An internal change, reordering of code without changing the public API.
[INTERNAL] Reordering code in module sequence so no more generated forwards are needed.
An internal change might include tests and improved comments.
[INTERNAL,TEST,COMMENTS] Greatly improved transmogrify module. Restructured the whole internal structure of the module, adding a large number of tests and improving the source-level documentation. The user level documentation is still lacking and should be the target of a future change.
Changes to the command line interface:
[CLI] Changed output of STELLAR such to unify scientific notation floats.
Changes to logging in an app:
[LOG] Improved logging in RazerS 5. Much more detailed logging allows easier debugging. Part of this should probably be commented out before the next stable release once the dust has settled and most bugs have been removed.