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#!/usr/bin/python3
import os
import shasta
import GetConfig
# Read the config file.
config = GetConfig.getConfig()
# Initialize the assembler and access what we need.
a = shasta.Assembler()
a.accessMarkers()
a.accessAlignmentDataReadWrite()
# Create the global read graph.
a.createReadGraph2(
maxAlignmentCount = int(config['ReadGraph']['maxAlignmentCount']),
markerCountPercentile = float(config['ReadGraph']['markerCountPercentile']),
alignedFractionPercentile = float(config['ReadGraph']['alignedFractionPercentile']),
maxSkipPercentile = float(config['ReadGraph']['maxSkipPercentile']),
maxDriftPercentile = float(config['ReadGraph']['maxDriftPercentile']),
maxTrimPercentile = float(config['ReadGraph']['maxTrimPercentile']))
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