Source code for hairpin2.const

# hairpin2
#
# Copyright (C) 2024, 2025 Genome Research Ltd.
#
# Author: Alex Byrne <ab63@sanger.ac.uk>
#
# 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
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
from enum import Enum, StrEnum




class ValidNucleotides(Enum):
    """
    VCF nucleotides, which hairpin2 is able to process.
    """

    ALL = {"A", "C", "T", "G", "N", "*"}





class Strand(StrEnum):
    """
    Enum used to indicate strandedness
    """

    BOTH = "BOTH"
    F = "F"
    R = "R"





class MutTypes(StrEnum):
    """
    VCF Variant types which hairpin2 is able to process.
    """

    SUB = "SUB"
    DEL = "DEL"
    INS = "INS"





class Tags(StrEnum):
    """
    Tags applied by additive read processors.
    """

    SUPPORT_TAG = "SUPPORTS-VAR"
    OVERLAP_TAG = "IS-OVERLAPPING-READ2"
    LOW_QUAL_TAG = "LOW-QUAL"
    STUTTER_DUP_TAG = "IS-STUTTER-DUP"





class TaggerNamespaces(StrEnum):
    """
    Process names for additive read processors (functions which add tag data to reads during execution).
    """

    MARK_SUPPORT = "mark-support"
    MARK_OVERLAP = "mark-overlap"
    MARK_LOW_QUAL = "mark-low-qual"
    MARK_STUTTER_DUP = "mark-duplicates"





class FlaggerNamespaces(StrEnum):
    """
    Process/Flag names for variant flaggers, which flag variants in the output VCF.
    """

    LOW_QUAL = "LQF"
    DUPLICATION = "DVF"
    POOR_ALIGNMENT_SCORE = "ALF"
    ANOMALOUS_DISTRIBUTION = "ADF"