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This software is a wrapper for MuMRescueLite by Faulkner, G.J., et al.
Bioinformatics (2009). The wrapper:

  • accepts SAM/BAM input
  • constructs the required input format required by MuMRescueLite
  • runs MuMRescueLite
  • outputs SAM/BAM file with the non-primary alignment reads from
    input removed

The MuMRescueLite.py script has also been converted to python3.

Required libraries:

  • docopt>=0.6.2
  • pysam>=0.9.1
  • marisa-trie>=0.7.2