API

pydamage.main.analyze(bam, fasta, 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

  • fasta (str) – Path to fasta file containing reference sequences

  • 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