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"""Utility functions for realigner."""

from third_party.nucleus.protos import cigar_pb2

CIGAR_ALIGN_OPS = [
    cigar_pb2.CigarUnit.ALIGNMENT_MATCH,
    cigar_pb2.CigarUnit.SEQUENCE_MATCH,
    cigar_pb2.CigarUnit.SEQUENCE_MISMATCH,
]
CIGAR_INSERT_OPS = [cigar_pb2.CigarUnit.INSERT, cigar_pb2.CigarUnit.CLIP_SOFT]
CIGAR_DELETE_OPS = [cigar_pb2.CigarUnit.DELETE, cigar_pb2.CigarUnit.SKIP]
CIGAR_NO_OPS = [cigar_pb2.CigarUnit.CLIP_HARD]

# Suppported cigar operations in realigner.
CIGAR_OPS = CIGAR_ALIGN_OPS + CIGAR_INSERT_OPS + CIGAR_DELETE_OPS + CIGAR_NO_OPS