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#!/usr/bin/python3
import shasta
import GetConfig
# Read the config file.
config = GetConfig.getConfig()
# Initialize the assembler and access what we need.
a = shasta.Assembler()
a.accessMarkerGraphVertices()
a.accessMarkerGraphEdges(accessEdgesReadWrite=True)
a.accessMarkerGraphReverseComplementEdge()
a.transitiveReduction(
lowCoverageThreshold = int(config['MarkerGraph']['lowCoverageThreshold']),
highCoverageThreshold = int(config['MarkerGraph']['highCoverageThreshold']),
maxDistance = int(config['MarkerGraph']['maxDistance']),
edgeMarkerSkipThreshold = int(config['MarkerGraph']['edgeMarkerSkipThreshold'])
)
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