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bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics
GNU Affero General Public License v3.0
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The components assembly module has to be "assembler agnostic" #24

Closed loic-couderc closed 7 years ago

loic-couderc commented 7 years ago

The components_assembly module has many references to SGA assembler. This references have to be removed.

Moreover, add an option in matam_assembly to choose the assembler.

loic-couderc commented 7 years ago

By the way, add a parser for command line options.

loic-couderc commented 7 years ago

@ppericard : Is there a will to expose assembler parameters to matam_assembly.py as different assembler can have different parameters?

ppericard commented 7 years ago

@loic-couderc You're right, we should not expose the assembler parameters, but we could have some kind of parameter (or a switch) to change the assembler sensitivity. E.g. a "--sensitive" switch that would set up the assembler parameters to be more sensitive (and take more time/ressources in that case). Or a "--fast" switch with the contrary effect. We also have to keep the "--read_correction" parameter in matam_assembly, since this could be independent of the chosen assembler.

loic-couderc commented 7 years ago

No "--sensitive" or "--fast" switch for the moment, but it should not be too hard to implement it if needed.