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vgteam / gssw

efficient alignment of strings to partially ordered string graphs
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Reworked traceback #6

Closed adamnovak closed 8 years ago

adamnovak commented 8 years ago

This PR brings in my new traceback code, which saves the E and F matrices and uses them during the traceback.

It also includes @AlexKuhnle's changes introducing 'X' and 'N' CIGAR operations, and adding file arguments to some of the print methods.

Closes #1.

ekg commented 8 years ago

@adamnovak this is awesome work. You have rescued GSSW from a confused place and brought the project very near to completion. We should think about writing this up as an application note or at least a preprint. It would only need to be a few pages as we could limit ourselves to a description of the generalization of SSW to POA.

adamnovak commented 8 years ago

More papers are always better.

For a paper, we should probably collect some speed comparisons with the original, to see what sort of impact the dumping of the matrices actually has. If we really are concerned about speed, we might consider dumping the striped matrices, and unscrambling later (or even never if we write code to find the correct elements to read).

On Sat, Apr 9, 2016 at 12:46 AM, Erik Garrison notifications@github.com wrote:

Merged #6 https://github.com/ekg/gssw/pull/6.

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