def _decode_post(post,
stay_pen=0.0,
skip_pen=0.0,
local_pen=2.0,
use_slip=False):
"""Decode a posterior using Viterbi algorithm for transducer.
:param post: a `ScrappyMatrix` containing transducer posteriors.
:param stay_pen: penalty for staying.
:param skip_pen: penalty for skipping a base.
:param local_pen: penalty for local basecalling.
:param use_slip: allow slipping (movement more than 2 bases).
:returns: tuple containing (call, score, call positions per raw block).
"""
nblock, nstate = post.shape
path = ffi.new("int[{}]".format(nblock + 1))
score = lib.decode_transducer(post.data(), stay_pen, skip_pen, local_pen,
path, use_slip)
pos = np.zeros(nblock + 1, dtype=np.int32)
p_pos = ffi.cast("int *", pos.ctypes.data)
basecall = lib.overlapper(path, nblock + 1, nstate - 1, p_pos)
return ffi.string(basecall).decode(), score, pos
def _decode_post_crf(post):
"""Decode a posterior using Viterbi algorithm for conditional random field.
:param post: a `ScrappyMatrix` containing CRF transitions.
:returns: tuple containing (basecall, score, call positions per raw data block).
"""
nblock, nstate = post.shape
path = ffi.new("int[{}]".format(nblock + 1))
score = lib.decode_crf(post.data(), path)
pos = np.ascontiguousarray(np.zeros(nblock + 1, dtype=np.int32))
p_pos = ffi.cast("int *", ffi.from_buffer(pos))
basecall = lib.crfpath_to_basecall(path, nblock, p_pos)
return ffi.string(basecall).decode(), score, pos