ccsmeth 0.3.0

Detecting DNA methylation from PacBio CCS reads

Documentation

v0.3.0

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

v0.2.3

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/)

v0.2.1

minor fixes

change default mode in extract module

improvements in call_freqb module

v0.2.0

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

v0.1.2

add pbmm2 as default aligner

enable gzip output

v0.1.1

bug fixes

v0.1.0

initialize