Add more options for tool parameterizations#1

Draft

ClaraUktar wants to merge 10 commits intomainfrom

feat/increased-tool-parameterization

Commits on Jun 2, 2024

Add coverage and identity constraints for GMAP
ClaraUktar
committed

Commits on Jun 23, 2024

Commits on Jul 2, 2024

Update gmap for linux
ClaraUktar
committed

Commits on Aug 19, 2024

Handle antisense direction during gtf creation
ClaraUktar
committed

Commits on Aug 29, 2024

WIP: Cut out contig parts based on alignment
ClaraUktar
committed

Commits on Sep 12, 2024

Rewrite CDS features based on exons
ClaraUktar
committed

Commits on Sep 20, 2024

Sort exons before rewrite to gtf
ClaraUktar
committed

Commits on Apr 5, 2025

WIP: Handle indels in alignment results
ClaraUktar
committed

Commits on Apr 6, 2025

Exclude alignments with indels if parameter active
ClaraUktar
committed