Source code for tsinfer.constants

#
# Copyright (C) 2018-2023 University of Oxford
#
# This file is part of tsinfer.
#
# tsinfer is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# tsinfer is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with tsinfer.  If not, see <http://www.gnu.org/licenses/>.
#
"""
Collection of constants used in tsinfer. We also make use of constants defined in tskit.
"""
import enum

import numpy as np

C_ENGINE = "C"
PY_ENGINE = "P"


# TODO Change these to use the enum.IntFlag class

# Bit 16 is set in node flags when they have been created by path compression.
NODE_IS_PC_ANCESTOR = np.uint32(1 << 16)
# Bit 17 is set in node flags when they have been created by shared recombination
# breakpoint
NODE_IS_SRB_ANCESTOR = np.uint32(1 << 17)
# Bit 18 is set in node flags when they are samples inserted to augment existing
# ancestors.
NODE_IS_SAMPLE_ANCESTOR = np.uint32(1 << 18)
# Bit 20 is set in node flags when they are samples not at time zero in the sampledata
# file
NODE_IS_HISTORICAL_SAMPLE = np.uint32(1 << 20)

# What type of inference have we done at a site?
INFERENCE_NONE = "none"
INFERENCE_FULL = "full"
INFERENCE_PARSIMONY = "parsimony"




class GenotypeEncoding(enum.IntEnum):
    """
    The encoding scheme used to store genotypes.
    """

    EIGHT_BIT = 0
    """
    The default approach of using one-byte per genotype. Supports up to 127 alleles
    and missing data.
    """

    ONE_BIT = 1
    """
    Encode binary genotype data using a single bit.
    """