Ccsmeth

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

optimize call_mods module

add aggregate mode in call_freqb module

release a stable call_mods model and a stable call_freqb aggregate model

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

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/)

minor fixes

change default mode in extract module

improvements in call_freqb module

use hifi reads instead of subreads as input

modbam support

use (chrom, pos, strand) as key instead of (chrom, pos) to handle CG mismatch in CCS read when call_freq