Pinned alignment and pinned multi-alignment

vgteam / gssw

efficient alignment of strings to partially ordered string graphs

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Pinned alignment and pinned multi-alignment #9

Closed jeizenga closed 8 years ago

jeizenga commented 8 years ago

Added new functions to perform alignment with a "pinned node", where the end of the read must be aligned to the end of the node. This is intended to be used in the MEM threading routine in vg. I also added the ability to return an arbitrary number of alternate pinned alignments in addition to the optimum. These are returned in descending score order from the optimum.

ekg commented 8 years ago

This repo does need tests... I guess we could just run vg's with the new gssw embedded :joy: