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"""Common constants shared across DeepVariant's codebase.

This file is for very general constants in the code that end up needing to be
accessed in a variety of places, often in live code as well as throughout the
code in tests.
"""

# Default width [in basepairs] for our DeepVariant data tensor.
PILEUP_DEFAULT_WIDTH = 221

# Default height [in rows] for our DeepVariant data tensor.
PILEUP_DEFAULT_HEIGHT = 100

# Not a default because it's hard-coded into the code.
PILEUP_NUM_CHANNELS = 6

# The dimensions of a pileup image tensor as height x width x rank.
PILEUP_DEFAULT_DIMS = [
    PILEUP_DEFAULT_HEIGHT,
    PILEUP_DEFAULT_WIDTH,
    PILEUP_NUM_CHANNELS,
]

# Number of classes represented in the data set. The three classes are
# homozygous reference (0), heterozygous (1) and homozygous alternative (2).
NUM_CLASSES = 3
NUM_DENOVO_CLASSES = 2

# Default sample name if no sample name is found from the BAM header.
DEFAULT_SAMPLE_NAME = 'default'

# Define available OptChannels (optional extra channels).
OPT_CHANNELS = [
    'read_base',
    'base_quality',
    'mapping_quality',
    'strand',
    'read_supports_variant',
    'base_differs_from_ref',
    'read_mapping_percent',
    'avg_base_quality',
    'identity',
    'gap_compressed_identity',
    'gc_content',
    'is_homopolymer',
    'homopolymer_weighted',
    'blank',
    'insert_size',
]

# Used only when phasing is on (phase_reads=true). It allows to set the
# region padding as a percantage over the region length. candidates are
# calculated over an extended region. Output examples are not affected by
# this value.
PHASE_READS_REGION_PADDING_PCT = 20