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#!/usr/bin/python3
import shasta
import GetConfig
import ast
import sys
# Read the config file.
config = GetConfig.getConfig()
# Initialize the assembler and access what we need.
a = shasta.Assembler()
a.accessKmers()
a.accessMarkers()
a.accessAlignmentData()
a.accessReadGraph()
a.accessCompressedAlignments()
# Do the computation.
a.createMarkerGraphVertices(
minCoverage = int(config['MarkerGraph']['minCoverage']),
maxCoverage = int(config['MarkerGraph']['maxCoverage']),
minCoveragePerStrand = int(config['MarkerGraph']['minCoveragePerStrand']),
allowDuplicateMarkers = ast.literal_eval(config['MarkerGraph']['allowDuplicateMarkers']),
peakFinderMinAreaFraction = float(config['MarkerGraph']['peakFinder.minAreaFraction']),
peakFinderAreaStartIndex = int(config['MarkerGraph']['peakFinder.areaStartIndex']))
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