Less stringent alignment and seed filtering - Githubissues

ratschlab / metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

http://metagraph.ethz.ch

GNU General Public License v3.0

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Less stringent alignment and seed filtering #453

Open hmusta opened 1 year ago

hmusta commented 1 year ago

No default limit on the total number of output alignments
If a seed has a filtered-out label, report the seed as an alignment without extending it
Annotate dummy node seeds with labels of their nearest annotated nodes
Introduce alignment chaining from MetaGraph-MLA

TODO

[x] Merge reported seeds into MEMs (since it outputs too much)
[x] When merging seeds with coordinates, ensure that the coordinates are consistent
[x] Figure out why some extensions are not happening
[x] Alignment is too slow and timing out, figure out why
[x] Chain together filtered-out seeds to cheaply get longer alignments