import numpy as np
[docs]def correct_read_position(flags, start_position, readlength):
"""Correct starting position for reads with reversed orientation
Parameters
----------
flags : numpy.array
[description]
start_position : numpy.array
[description]
readlength : numpy.array
[description]
Returns
-------
numpy.array
start position and flags corrected
"""
flag0coor_array = np.where(flags == 1) # coordinates reads 5' -> 3'
flag16coor_array = np.where(flags == -1) # coordinates reads 3' -> 5'
startdirect_array = start_position[flag0coor_array]
flagdirect_array = flags[flag0coor_array]
startindirect_array = (
start_position[flag16coor_array] + readlength[flag16coor_array]
)
flagindirect_array = flags[flag16coor_array]
start_position_corrected = np.concatenate(
(startdirect_array, startindirect_array), axis=0
)
flags_corrected = np.concatenate((flagdirect_array, flagindirect_array), axis=0)
start_sortindices = start_position_corrected.argsort(
kind="mergesort"
) # use mergesort for stable sorting
start_position_corrected = start_position_corrected[start_sortindices]
flags_corrected = flags_corrected[start_sortindices]
return start_position_corrected, flags_corrected
