text: #!/usr/bin/python3
  
  import shasta
  import GetConfig
  import sys
  
  # Read the config file.
  config = GetConfig.getConfig()
  
  # Initialize the assembler and access what we need.
  a = shasta.Assembler()
  a.accessKmers()
  a.accessMarkers()
  a.accessAlignmentCandidates()
  
  # Do the computation.
  a.computeAlignmentsGpu(
      maxMarkerFrequency = int(config['Align']['maxMarkerFrequency']),
      maxSkip = int(config['Align']['maxSkip']),
      minAlignedMarkerCount = int(config['Align']['minAlignedMarkerCount']),
      maxTrim = int(config['Align']['maxTrim']))
  
  