`FermiAssembler` should take `fml_opt_t` assembly parameters from the user.

walaj / SeqLib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

http://bioinformatics.oxfordjournals.org/content/early/2016/12/21/bioinformatics.btw741.full.pdf+html

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`FermiAssembler` should take `fml_opt_t` assembly parameters from the user. #59

Closed cgroza closed 3 years ago

cgroza commented 3 years ago

Hi,

Sometimes the user needs to finely tune their assembly parameters for their own purposes. The best way to do this is to construct their own fml_opt_t structure and pass it to FermiAssembler. I added a constructor that implements this and also exposed another flag for graph simplification.

Hope these changes are useful, Cristian Groza

walaj commented 3 years ago

This looks reasonable, you're probably much closer to a setup to actively test this than I am these days. Thanks for exposing this option.