Phylign
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Add a possibility to plug another mapper
- 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.)