CLI
To access the help menu:
$ pydamage --help
The list of arguments of options is detailed below
pydamage
pydamage [OPTIONS] COMMAND [ARGS]...
Options
- --version
Show the version and exit.
- -o, --outdir <outdir>
Output directory
- Default:
'pydamage_results'
- -t, --threshold <threshold>
Predicted accuracy filtering threshold. Set to 0 for finding threshold with kneed method
- Default:
0.5
analyze
BAM: path to BAM/SAM/CRAM alignment file. MD tags need to be set.
pydamage analyze [OPTIONS] BAM
Options
- -w, --wlen <wlen>
Window length (in bp) for damage modeling
- Default:
13
- -m, --minlen <minlen>
Minimum of length of reference sequence to consider
- Default:
0
- -p, --process <process>
Number of processes for parallel computing
- Default:
2
- -s, --show_al
Display alignments representations
- -pl, --plot
Write damage fitting plots to disk
- -vv, --verbose
Verbose mode
- -f, --force
Force overwriting of results directory
- -g, --group
Use entire BAM file as single reference for analysis (ignore reference headers)
- -n, --no_ga
Do not use G->A transitions
- -r, --rescale
Rescale base quality scores using the PyDamage damage model NOTE: This argument is mutually exclusive with arguments: [subsample].
- -s, --subsample <subsample>
Subsample a fraction of the reads for damage modeling NOTE: This argument is mutually exclusive with arguments: [rescale].
Arguments
- BAM
Required argument
cite
Get pydamage citation in bibtex format
pydamage cite [OPTIONS]
filter
CSV: path to PyDamage result file
pydamage filter [OPTIONS] CSV
Arguments
- CSV
Required argument