API¶
- pydamage.main.analyze_group(bam, wlen=30, show_al=False, process=1, outdir='', plot=False, verbose=False, force=False)[source]¶
Runs the pydamage analysis with all references grouped as one
- Parameters
bam (str) – Path to alignment (sam/bam/cram) file
wlen (int) – window length
show_al (bool) – print alignments representations
process (int) – Number of processes for parellel computing
outdir (str) – Path to output directory
verbose (bool) – verbose mode
force (bool) – force overwriting of results directory
- Returns
pandas DataFrame containg pydamage results
- Return type
pd.DataFrame
- pydamage.main.analyze_multi(bam, wlen=30, show_al=False, process=1, outdir='', plot=False, verbose=False, force=False)[source]¶
Runs the pydamage analysis for each reference separately
- Parameters
bam (str) – Path to alignment (sam/bam/cram) file
wlen (int) – window length
show_al (bool) – print alignments representations
process (int) – Number of processes for parellel computing
outdir (str) – Path to output directory
verbose (bool) – verbose mode
force (bool) – force overwriting of results directory
- Returns
pandas DataFrame containg pydamage results
- Return type
pd.DataFrame