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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.accessAlignmentData()
a.accessMarkerGraphVertices()
a.accessMarkerGraphEdges()
a.accessAssemblyGraphVertices()
a.accessAssemblyGraphEdges()
a.accessAssemblyGraphEdgeLists()
# Create the read graph.
a.createReadGraphUsingPseudoPaths(
matchScore = int(config['Assembly']['iterative.pseudoPathAlignMatchScore']),
mismatchScore = int(config['Assembly']['iterative.pseudoPathAlignMismatchScore']),
gapScore = int(config['Assembly']['iterative.pseudoPathAlignGapScore']),
mismatchSquareFactor = int(config['Assembly']['iterative.mismatchSquareFactor']),
minScore = int(config['Assembly']['iterative.minScore']),
maxAlignmentCount = int(config['Assembly']['iterative.maxAlignmentCount']))
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