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#!/usr/bin/python3
import shasta
import argparse
parser = argparse.ArgumentParser(description=
'Set the flags of all marker graph edges to specified values, or specify 2 to leave a flag unchanged.')
parser.add_argument('--wasRemovedByTransitiveReduction', type=int, default=2, choices=range(3))
parser.add_argument('--wasPruned', type=int, default=2, choices=range(3))
parser.add_argument('--isSuperBubbleEdge', type=int, default=2, choices=range(3))
parser.add_argument('--isLowCoverageCrossEdge', type=int, default=2, choices=range(3))
parser.add_argument('--wasAssembled', type=int, default=2, choices=range(3))
arguments = parser.parse_args()
a = shasta.Assembler()
a.accessMarkerGraphEdges(accessEdgesReadWrite = True)
a.setMarkerGraphEdgeFlags(
wasRemovedByTransitiveReduction = arguments.wasRemovedByTransitiveReduction,
wasPruned = arguments.wasPruned,
isSuperBubbleEdge = arguments.isSuperBubbleEdge,
isLowCoverageCrossEdge = arguments.isLowCoverageCrossEdge,
wasAssembled = arguments.wasAssembled)
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