bwapy package

Submodules

bwapy.libbwa module

class bwapy.libbwa.Alignment(rname, orient, pos, mapq, cigar, NM)

Bases: tuple

NM

Alias for field number 5

cigar

Alias for field number 4

mapq

Alias for field number 3

orient

Alias for field number 1

pos

Alias for field number 2

rname

Alias for field number 0

class bwapy.libbwa.BwaAligner(index: str, options: str = '')

Bases: object

align_seq(seq: str)

Align a sequence to the index.

Parameters:seq – base sequence to align Returns:tuple of Alignment

bwapy.libbwa.ffi = <cffi.api.FFI object>

High-level interface to bwa (mem) aligner.

bwapy.libbwa.get_parser()

bwapy.libbwa.get_shared_lib(name)

Cross-platform resolution of shared-object libraries, working around vagueries of setuptools. :param name: name of shared library to find.

Returns:FFI shared library object.

bwapy.libbwa.main()

Module contents