README.rst

deepsignal-plant

Release

0.1.7

optimize/test more on multi-gpu support in call_mods module

add scipy==1.7.3 in requirements (floating point error in scipy>=1.9->tombo). fix this in deepsignal-plant, although tombo only is the pre-process tool for this tool.

replace np.float/np.int with float/int in extract_features module

0.1.6

bug fixes

enable .gz output in extract/call_mods/call_freq modules

multi-gpu support in call_mods module

update requirements/dependences

0.1.5

make sure results of each read be written together in call_mods' output

make --reference_path not a required input in extract and call_mods module

0.1.4

modify call_freq module for large genomes,

fix bug of extrating contig name from fast5s

0.1.3

add ranger optimizer and modify train module,

fix Queue.qsize() NotImplementedError in macOS partially, however call_mods in CUDA mode in macOS still doesn't work,

add init_model option in train module

0.1.2

change imports in ref_reader,

change requirements,

fix and modify denoise module,

fix MKL_THREADING_LAYER error temporarily,

add --region option,

a combined 5mC model replacing CG/CHG/CHH models

0.1.1

fix bug and optimize call_mods without GPU, add call_freq funciton

0.1.0

Release the first vesrion of deepsignal-plant package