API Documentation

This includes a thorough documentation of all pertinent modules, functions, and classes contained within ssw-py.

• ssw.alignmentmgr
• AlignmentMgr
  • AlignmentMgr.read
  • AlignmentMgr.reference
  • AlignmentMgr.match_score
  • AlignmentMgr.mismatch_penalty
  • AlignmentMgr.align()
  • AlignmentMgr.build_dna_score_matrix()
  • AlignmentMgr.match_score
  • AlignmentMgr.mismatch_penalty
  • AlignmentMgr.printResult()
  • AlignmentMgr.print_result()
  • AlignmentMgr.setRead()
  • AlignmentMgr.setReference()
  • AlignmentMgr.set_read()
  • AlignmentMgr.set_reference()
• BitwiseAlignmentFlag
  • BitwiseAlignmentFlag.best_idxs_no_cigar
  • BitwiseAlignmentFlag.distance_filter
  • BitwiseAlignmentFlag.score_filter
  • BitwiseAlignmentFlag.best_idxs
  • BitwiseAlignmentFlag.end_idxs_only_no_cigar
• force_align()
• format_force_align()
• ssw.alignmenttuple
• Alignment
  • Alignment.CIGAR
  • Alignment.optimal_score
  • Alignment.sub_optimal_score
  • Alignment.reference_start
  • Alignment.reference_end
  • Alignment.read_start
  • Alignment.read_end
  • Alignment.cigar_pair_list
• ssw.printer
• printer()