File: SplitMarkerGraphSecondaryEdges.py

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#!/usr/bin/python3

import shasta
import GetConfig

config = GetConfig.getConfig()

a = shasta.Assembler()

a.accessMarkers()
a.accessMarkerGraphEdges(True, True)
a.accessMarkerGraphReverseComplementEdge()

a.splitMarkerGraphSecondaryEdges(
    errorRateThreshold = float(config['MarkerGraph']['secondaryEdges.split.errorRateThreshold']),
    minCoverage = int(float(config['MarkerGraph']['secondaryEdges.split.minCoverage'])
    )