Closed akikuno closed 3 months ago
Remove multi-mapping reads, as multi-mapping reads are mostly reads that are locally mapped to low-complexity regions. Commit Detail
Create preprocess.input_formatter.py to summarize formatting functions to a module. Commit Detail
preprocess.input_formatter.py
Refactor directory_manager.py Commit Detail
directory_manager.py
Refactor preprocess.__init__.py Commit Detail
preprocess.__init__.py
To increase cohesion by functions of the same category into a single module, we have migrated preprocess.fastx_parser to utils.fastx_handler. Commit Detail
preprocess.fastx_parser
utils.fastx_handler
Remove the packages that are no longer in use from requirements.txt. Commit Detail
requirements.txt
Add read_sam in sam_handler module. Commit Detail
read_sam
Revise the docstring of export_fasta_files. Commit Detail
export_fasta_files
Standardize to use dataclass instead of NamedTuple. Commit Detail
dataclass
NamedTuple
🔧 Maintenance
Remove multi-mapping reads, as multi-mapping reads are mostly reads that are locally mapped to low-complexity regions. Commit Detail
Create
preprocess.input_formatter.pyto summarize formatting functions to a module. Commit DetailRefactor
directory_manager.pyCommit DetailRefactor
preprocess.__init__.pyCommit DetailTo increase cohesion by functions of the same category into a single module, we have migrated
preprocess.fastx_parsertoutils.fastx_handler. Commit DetailRemove the packages that are no longer in use from
requirements.txt. Commit DetailAdd
read_samin sam_handler module. Commit DetailRevise the docstring of
export_fasta_files. Commit DetailStandardize to use
dataclassinstead ofNamedTuple. Commit Detail