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#!/usr/bin/python3
import shasta
import GetConfig
import ast
# Read the config file.
config = GetConfig.getConfig()
# Create the Assembler.
a = shasta.Assembler()
# Set up the consensus caller.
a.setupConsensusCaller(config['Assembly']['consensusCaller'])
# Access what we need.
a.accessKmers()
a.accessMarkers()
a.accessMarkerGraphVertices()
a.accessMarkerGraphEdges(accessEdgesReadWrite = True)
a.accessAssemblyGraphVertices()
a.accessAssemblyGraphEdges()
# Do it.
assembleAllEdges = (int(config['Assembly']['mode']) == 2)
a.assembleMarkerGraphEdges(
markerGraphEdgeLengthThresholdForConsensus =
int(config['Assembly']['markerGraphEdgeLengthThresholdForConsensus']),
storeCoverageData = ast.literal_eval(config['Assembly']['storeCoverageData']),
assembleAllEdges = assembleAllEdges)
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