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#!/usr/bin/python3
import shasta
import GetConfig
import sys
helpMessage = """
This computes a marker alignment of two oriented reads.
Invoke with four arguments: readId0, strand0, readId1, strand1.
"""
# Get the arguments.
if not len(sys.argv) == 5:
print(helpMessage)
exit(1)
readId0 = int(sys.argv[1]);
strand0 = int(sys.argv[2]);
readId1 = int(sys.argv[3]);
strand1 = int(sys.argv[4]);
# Read the config file.
config = GetConfig.getConfig()
# Initialize the assembler and access what we need.
a = shasta.Assembler()
a.accessKmers()
a.accessMarkers()
# For convenience, write the markers sorted by position.
a.writeMarkers(readId=readId0, strand=strand0,
fileName = 'Markers-ByPosition-0.csv')
a.writeMarkers(readId=readId1, strand=strand1,
fileName = 'Markers-ByPosition-1.csv')
# Compute the alignment.
a.alignOrientedReads(
readId0 = readId0, strand0 = strand0,
readId1 = readId1, strand1 = strand1,
maxSkip = int(config['Align']['maxSkip']),
maxDrift = int(config['Align']['maxDrift']),
maxMarkerFrequency = int(config['Align']['maxMarkerFrequency']))
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