API

pydamage.main.analyze(bam, wlen=30, show_al=False, mini=2000, cov=0.5, process=1, outdir='', plot=False, verbose=False, force=False)[source]

Runs the pydamage analysis

Parameters:
  • bam (str) – Path to alignment (sam/bam/cram) file
  • wlen (int) – window length
  • show_al (bool) – print alignments representations
  • mini (int) – Minimum numbers of reads aligned to consider contigs
  • cov (float) – Minimum coverage to consider contig
  • 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