Implementation of soft-clipping and CIGAR computation#25

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haghshenas wants to merge 23 commits intoCOMBINE-lab:developfrom

OceanGenomics:soft-clip

Commits on Sep 15, 2022

initial implementation of soft clipping

Ehsan Haghshenas
authored and
Hossein Asghari
committed
fix the alignment start position

Ehsan Haghshenas
authored and
Hossein Asghari
committed
better command line interface

Ehsan Haghshenas
authored and
Hossein Asghari
committed
added end_bonus and end2end user arguments
Hossein Asghari
committed
maximum softclip threshold implemented
Hossein Asghari
committed
untangle allowSoftclip and computeCIGAR parameters
Hossein Asghari
committed
integrate cigar generation
Hossein Asghari
committed
alignment acceptance based on not soft-clipped length
Hossein Asghari
committed
end_bonus parentheses
Hossein Asghari
committed
reset softclip variables
Hossein Asghari
committed
fixed target length bug for left and right extension
Hossein Asghari
committed
make computeCIGAR independent from allowSoftclip feature
Hossein Asghari
committed
pass logger to deeper functions
Hossein Asghari
committed

Commits on Sep 18, 2022

clean up

Ehsan Haghshenas
authored and
Hossein Asghari
committed
reset ez object for every alignment
Hossein Asghari
committed
properly cache soft-clipped alignments
Hossein Asghari
committed
fix cutoff issue in case of softclipping
Hossein Asghari
committed
full alignment softclipping
Hossein Asghari
committed
separate sotfclip fraction for general and overhanging cases
Hossein Asghari
committed
removed endBonus from alignment config
Hossein Asghari
committed
max softclip fraction help message
Hossein Asghari
committed
max softclip fraction help message
Hossein Asghari
committed
better separate overhang and general cases; handle complex general and overhang cases happening together
Hossein Asghari
committed