Simplify the insertion of the polymorphism in the fasta sequence for VCF inputs
Currently, the getFasta
process adds a complex header with -name
(ex: Lcu.2RBY.Chr1_58402_A_G::Lcu.2RBY.Chr1:58301-58502) with the first part before the "::" being the original ID. This header is used to locate where the relative position of the polymorphism is for the insertion of the ref/alt sequences. However, there is now a parameter for the slop size that can be used for that purpose.
- Use the slop parameter as an input for the
add_ref_alt_in_seq.py
- Replace the
-name
by-nameOnly
in thegetFasta
process (<=> keep the original ID) - Remove the process to trim the getFasta complex ID
Edited by Baptiste Imbert