ccsmeth 0.5.0

Description:

ccsmeth 0.5.0

Changelog


v0.5.0
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


v0.4.1
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


v0.4.0
optimieze call_mods module, faster generating of modbam file


v0.3.4
replace ‘numpy.float’ by ‘float” in extract_features and call_mods modules


v0.3.3
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)


v0.3.2
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


v0.3.1
optimize call_mods module
add aggregate mode in call_freqb module
release a stable call_mods model and a stable call_freqb aggregate model


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