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Add a possibility to plug another mapper #231

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karel-brinda opened this issue Nov 2, 2023 · 0 comments

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karel-brinda commented Nov 2, 2023 •

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Based on one of the reviewers comments
A bit tricky – not all mappers can work in 1 command
The way to go: create a bash script align_to_genome.sh [params] ref.fa query.fa
Still have to somehow handle passing minimap2 presets to this

Phases:

clean the current batch_align.py (copying to deprec for archivation and removing all unused functions so that we modify only the relevant ones)
create align_to_genome.sh
adjust configuration

Users then can modify align_to_genome.sh if they want to use a custom read mapper (experimentally).

(All this should be relatively simple. If not, we shouldn't implement it.)

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karel-brinda added the enhancement label

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