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#!/usr/bin/python3
import shasta
import argparse
import GetConfig
# Read the config file.
config = GetConfig.getConfig()
# Parse the command line arguments.
parser = argparse.ArgumentParser(description=
'Run Mode 3 assembly starting from the marker graph.')
parser.add_argument(
"--debug",
dest="debug",
action="store_true",
)
arguments = parser.parse_args()
# Open a performance log.
shasta.openPerformanceLog('Mode3Assembly.log')
# Create the Assembler object and access what we need.
options = shasta.AssemblerOptions('shasta.conf')
a = shasta.Assembler()
a.accessMarkers()
# Run Mode 3 assembly using existing Anchors.
a.mode3Reassembly(0, options.assemblyOptions.mode3Options, arguments.debug)
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