aldro61

# Generate a logspace from numpy in bash
# Usage: logspace start end [count, default=10]
# Just source this file or add it to your .bashrc
logspace () {
    start=$1
    end=$2
    if [ $# -ne 3 ]
    then
        count=10
    else

aldro61

"""
Load the MNIST dataset into numpy arrays

Author: Alexandre Drouin
License: BSD

"""
import numpy as np

from tensorflow.examples.tutorials.mnist import input_data

aldro61

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aldro61

def load_hic_matrix(hic_path):
    f = open(hic_path, "r")
    
    # Parse the header
    header = f.next()
    assert header[0] == "#"
    min_row, max_row, min_col, max_col = [int(x) for x in header[2:].split(" ")]
    
    # Create an empty matrix of n_fragments x n_fragments
    hic = np.zeros((max_col + 1, max_col + 1))

aldro61

"""
Compile with gcc flag -mpopcnt
"""
import numpy as np
cimport numpy as np
cimport cython
from libc.stdint cimport uint32_t, uint8_t

cdef extern int __builtin_popcount(unsigned int) nogil

aldro61

#  Copyright (c) 2013 Alexandre Drouin. All rights reserved.
#
#  Permission is hereby granted, free of charge, to any person obtaining a copy of
#  this software and associated documentation files (the "Software"), to deal in
#  the Software without restriction, including without limitation the rights to
#  use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
#  of the Software, and to permit persons to whom the Software is furnished to do
#  so, subject to the following conditions:
#
#  The above copyright notice and this permission notice shall be included in all