0.5.0

bug fixes

change feature QUAL to SNratio, didn't work though?

hid '--n_vocab' and '--n_embed' in model params

add attbigru2s2/attbilstm2s2 models

update new version of pretrained model params

0.4.1

handle ValueError when fetching bam items in call_freqb module

change pytorch max version to 1.12.1

using logging instead of print/sys.stderr.write

0.4.0

optimieze call_mods module, faster generating of modbam file

0.3.4

replace 'numpy.float' by 'float" in extract_features and call_mods modules

0.3.3

more robust operation for MM/ML tags

update the call_mods model (v1 to v2), use shared params for both rnn and attention

update aggregate model (v2 to v2p)

0.3.2

fix bug (0-pos CG in reverse strand) of call_freqb module

add output check at the start of call_mods/call_freqb

update aggregate model

0.3.1

optimize call_mods module

add aggregate mode in call_freqb module

release a stable call_mods model and a stable call_freqb aggregate model

0.3.0

add multi-threads support for reading .bam by pysam

force mod prob discrete integer in [0, 255], which means mod prob in [0, 1), in ML tag

fix align_hifi module, enable minimap2 and bwa

update requirements

0.2.3

more options in train module

multi-gpu support in call_mods and trainm modules

add denoise module

Note: skip 0.2.2, cause 0.2.2 has been deleted in pypi (https://pypi.org/manage/project/ccsmeth/history/)

0.2.1

minor fixes

change default mode in extract module

improvements in call_freqb module