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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.accessMarkers()
a.accessAlignmentData()
a.accessCompressedAlignments()
a.accessMarkerGraphVertices(readWriteAccess = True)
a.accessMarkerGraphReverseComplementVertex(readWriteAccess = True)
a.cleanupDuplicateMarkers(
minCoverage = a.getMarkerGraphMinCoverageUsed(),
minCoveragePerStrand = int(config['MarkerGraph']['minCoveragePerStrand']),
duplicateMarkersPattern1Threshold = float(config['MarkerGraph']['duplicateMarkersPattern1Threshold']),
pattern1CreateNewVertices = False,
pattern2CreateNewVertices = False)
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