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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.

"""

from deepvariant.protos import deepvariant_pb2

# 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

# Default channels if none are provided

PILEUP_DEFAULT_CHANNELS = [

    'read_base',

    'base_quality',

    'mapping_quality',

    'strand',

    'read_supports_variant',

    'base_differs_from_ref',

]

# Channels that include insert size.

PILEUP_CHANNELS_WITH_INSERT_SIZE = [

    'read_base',

    'base_quality',

    'mapping_quality',

    'strand',

    'read_supports_variant',

    'base_differs_from_ref',

    'insert_size',

]

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

PILEUP_NUM_CHANNELS = len(PILEUP_DEFAULT_CHANNELS)

# 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 all available channels, configured using --channel_list

CHANNELS = [

    'read_base',

    'base_quality',

    'mapping_quality',

    'strand',

    'read_supports_variant',

    'base_differs_from_ref',

    'haplotype',

    'allele_frequency',

    'diff_channels_alternate_allele_1',

    'diff_channels_alternate_allele_2',

    'read_mapping_percent',

    'avg_base_quality',

    'identity',

    'gap_compressed_identity',

    'gc_content',

    'is_homopolymer',

    'homopolymer_weighted',

    'blank',

    'insert_size',

    'base_channels_alternate_allele_1',

    'base_channels_alternate_allele_2',

    'mean_coverage',

]

ALT_ALIGNED_PILEUP_CHANNELS = [

    'base_channels_alternate_allele_1',

    'base_channels_alternate_allele_2',

    'diff_channels_alternate_allele_1',

    'diff_channels_alternate_allele_2',

]

# Create list of channels that can be used with --channel_list by removing

# channels specified using --alt_aligned_pileup.

USER_SET_CHANNELS = [

    x for x in CHANNELS if x not in ALT_ALIGNED_PILEUP_CHANNELS

]

CHANNEL_ENUM_TO_STRING = {

    deepvariant_pb2.CH_READ_BASE: 'read_base',

    deepvariant_pb2.CH_BASE_QUALITY: 'base_quality',

    deepvariant_pb2.CH_MAPPING_QUALITY: 'mapping_quality',

    deepvariant_pb2.CH_STRAND: 'strand',

    deepvariant_pb2.CH_READ_SUPPORTS_VARIANT: 'read_supports_variant',

    deepvariant_pb2.CH_BASE_DIFFERS_FROM_REF: 'base_differs_from_ref',

    deepvariant_pb2.CH_HAPLOTYPE_TAG: 'haplotype',

    deepvariant_pb2.CH_ALLELE_FREQUENCY: 'allele_frequency',

    deepvariant_pb2.CH_DIFF_CHANNELS_ALTERNATE_ALLELE_1: (

        'diff_channels_alternate_allele_1'

    ),

    deepvariant_pb2.CH_DIFF_CHANNELS_ALTERNATE_ALLELE_2: (

        'diff_channels_alternate_allele_2'

    ),

    deepvariant_pb2.CH_READ_MAPPING_PERCENT: 'read_mapping_percent',

    deepvariant_pb2.CH_AVG_BASE_QUALITY: 'avg_base_quality',

    deepvariant_pb2.CH_IDENTITY: 'identity',

    deepvariant_pb2.CH_GAP_COMPRESSED_IDENTITY: 'gap_compressed_identity',

    deepvariant_pb2.CH_GC_CONTENT: 'gc_content',

    deepvariant_pb2.CH_IS_HOMOPOLYMER: 'is_homopolymer',

    deepvariant_pb2.CH_HOMOPOLYMER_WEIGHTED: 'homopolymer_weighted',

    deepvariant_pb2.CH_BLANK: 'blank',

    deepvariant_pb2.CH_INSERT_SIZE: 'insert_size',

    deepvariant_pb2.CH_BASE_CHANNELS_ALTERNATE_ALLELE_1: (

        'base_channels_alternate_allele_1'

    ),

    deepvariant_pb2.CH_BASE_CHANNELS_ALTERNATE_ALLELE_2: (

        'base_channels_alternate_allele_2'

    ),

    deepvariant_pb2.CH_MEAN_COVERAGE: 'mean_coverage',

}

# 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