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#!/usr/bin/python3
import shasta
import GetConfig
import sys
helpMessage = """
This computes a marker alignment of two oriented reads
using alignment method 4.
Invoke with four arguments: readId0, strand0, readId1, strand1.
"""
# Get the arguments.
import argparse
parser = argparse.ArgumentParser(
description='This computes a marker alignment of two oriented reads using alignment method 4.')
parser.add_argument('readId0', type=int)
parser.add_argument('strand0', type=int, choices=range(2))
parser.add_argument('readId1', type=int)
parser.add_argument('strand1', type=int, choices=range(2))
arguments = parser.parse_args()
# Read the config file.
config = GetConfig.getConfig()
# Initialize the assembler and access what we need.
a = shasta.Assembler()
a.accessMarkers()
# This can fail if sorted markers are not avaialble, in which
# case alignOrientedReads4 computes sorted markers on the fly.
a.accessSortedMarkers()
# Compute the alignment.
a.alignOrientedReads4(
readId0 = arguments.readId0, strand0 = arguments.strand0,
readId1 = arguments.readId1, strand1 = arguments.strand1,
deltaX = int(config['Align']['align4.deltaX']),
deltaY = int(config['Align']['align4.deltaY']),
minEntryCountPerCell = int(config['Align']['align4.minEntryCountPerCell']),
maxDistanceFromBoundary = int(config['Align']['align4.maxDistanceFromBoundary']),
minAlignedMarkerCount = int(config['Align']['minAlignedMarkerCount']),
minAlignedFraction = float(config['Align']['minAlignedFraction']),
maxSkip = int(config['Align']['maxSkip']),
maxDrift = int(config['Align']['maxDrift']),
maxTrim = int(config['Align']['maxTrim']),
maxBand = int(config['Align']['maxBand']),
matchScore = int(config['Align']['matchScore']),
mismatchScore = int(config['Align']['mismatchScore']),
gapScore = int(config['Align']['gapScore']))
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