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"""Step one of DeepVariant: creates tf.Example protos for training/calling."""

import os
from absl import app
from absl import flags

from deepvariant import dv_constants

from deepvariant import logging_level
from deepvariant import make_examples_core
from deepvariant import make_examples_options
from deepvariant.protos import deepvariant_pb2
from third_party.nucleus.io.python import hts_verbose

from third_party.nucleus.util import errors
from third_party.nucleus.util import proto_utils

# Sentinel command line flag value indicating no downsampling should occur.
NO_DOWNSAMPLING = 0.0

MAIN_SAMPLE_INDEX = 0  # 0 is the only sample.

FLAGS = flags.FLAGS

# Adopt more general flags from make_examples_options.
flags.adopt_module_key_flags(make_examples_options)

# Flags related to the sample in DeepVariant:
READS_ = flags.DEFINE_string(
    'reads',
    None,
    (
        'Required. Aligned, sorted, indexed BAM file containing the reads we'
        ' want to call. Should be aligned to a reference genome compatible with'
        ' --ref. Can provide multiple BAMs (comma-separated).'
    ),
)
SAMPLE_NAME_ = flags.DEFINE_string(
    'sample_name',
    '',
    (
        'Sample name to use for our sample_name in the output'
        ' Variant/DeepVariantCall protos. If not specified, will be inferred'
        ' from the header information from --reads.'
    ),
)
PILEUP_IMAGE_HEIGHT_ = flags.DEFINE_integer(
    'pileup_image_height',
    0,
    'Height for the pileup image. If 0, uses the default height',
)
DOWNSAMPLE_FRACTION_ = flags.DEFINE_float(
    'downsample_fraction',
    NO_DOWNSAMPLING,
    (
        f'If not {NO_DOWNSAMPLING} must be a value between 0.0 and 1.0. Reads'
        ' will be kept (randomly) with a probability of downsample_fraction'
        ' from the input BAM. This argument makes it easy to create examples'
        ' as though the input BAM had less coverage.'
    ),
)
PROPOSED_VARIANTS_ = flags.DEFINE_string(
    'proposed_variants',
    '',
    (
        '(Only used when --variant_caller=vcf_candidate_importer.) '
        'Tabix-indexed VCF file containing the proposed positions and alts for '
        '`vcf_candidate_importer`. The GTs will be ignored.'
    ),
)
CANDIDATE_POSITIONS_ = flags.DEFINE_string(
    'candidate_positions',
    None,
    'Path to the binary file containing candidate positions.',
)


def one_sample_from_flags(add_flags=True, flags_obj=None):
  """Collect sample-related options into a list of samples."""
  # Sample-specific options.
  sample_name = make_examples_core.assign_sample_name(
      sample_name_flag=SAMPLE_NAME_.value, reads_filenames=READS_.value
  )
  sample_options = deepvariant_pb2.SampleOptions(
      role='main_sample',
      name=sample_name,
      variant_caller_options=make_examples_core.make_vc_options(
          sample_name=sample_name, flags_obj=flags_obj
      ),
      order=[0],
      pileup_height=dv_constants.PILEUP_DEFAULT_HEIGHT,
  )

  if add_flags:
    if READS_.value:
      sample_options.reads_filenames.extend(READS_.value.split(','))
    if DOWNSAMPLE_FRACTION_.value != NO_DOWNSAMPLING:
      sample_options.downsample_fraction = DOWNSAMPLE_FRACTION_.value
    if PILEUP_IMAGE_HEIGHT_.value:
      sample_options.pileup_height = PILEUP_IMAGE_HEIGHT_.value
    if PROPOSED_VARIANTS_.value:
      sample_options.proposed_variants_filename = PROPOSED_VARIANTS_.value
    if CANDIDATE_POSITIONS_.value:
      sample_options.candidate_positions = CANDIDATE_POSITIONS_.value
  samples_in_order = [sample_options]
  sample_role_to_train = sample_options.role
  return samples_in_order, sample_role_to_train


def default_options(add_flags=True, flags_obj=None):
  """Creates a MakeExamplesOptions proto populated with reasonable defaults.

  Args:
    add_flags: bool. defaults to True. If True, we will push the value of
      certain FLAGS into our options. If False, those option fields are left
      uninitialized.
    flags_obj: object.  If not None, use as the source of flags, else use global
      FLAGS.

  Returns:
    deepvariant_pb2.MakeExamplesOptions protobuf.

  Raises:
    ValueError: If we observe invalid flag values.
  """
  if not flags_obj:
    flags_obj = FLAGS

  samples_in_order, sample_role_to_train = one_sample_from_flags(
      add_flags=add_flags, flags_obj=flags_obj
  )

  options = make_examples_options.shared_flags_to_options(
      add_flags=add_flags,
      flags_obj=flags_obj,
      samples_in_order=samples_in_order,
      sample_role_to_train=sample_role_to_train,
      main_sample_index=MAIN_SAMPLE_INDEX,
  )

  if add_flags:
    options.bam_fname = os.path.basename(READS_.value)
  return options


def check_options_are_valid(options):
  """Checks that all the options chosen make sense together."""

  # Check for general flags (shared for DeepVariant and DeepTrio).
  make_examples_options.check_options_are_valid(
      options, main_sample_index=MAIN_SAMPLE_INDEX
  )

  main_sample = options.sample_options[MAIN_SAMPLE_INDEX]
  if (
      options.mode == deepvariant_pb2.MakeExamplesOptions.CANDIDATE_SWEEP
      and main_sample.candidate_positions is None
  ):
    errors.log_and_raise(
        '--candidate_positions is required when --positions_sweep is set.'
    )
  if (
      options.mode == deepvariant_pb2.MakeExamplesOptions.CANDIDATE_SWEEP
      and main_sample.proposed_variants_filename
  ):
    errors.log_and_raise(
        '--positions_sweep_mode is incompatible with --proposed_variants'
    )
  if main_sample.candidate_positions and main_sample.proposed_variants_filename:
    errors.log_and_raise(
        '--candidate_positions is incompatible with --proposed_variants'
    )


def main(argv=()):
  with errors.clean_commandline_error_exit():
    if len(argv) > 1:
      errors.log_and_raise(
          'Command line parsing failure: make_examples does not accept '
          'positional arguments but some are present on the command line: '
          '"{}".'.format(str(argv)),
          errors.CommandLineError,
      )
    del argv  # Unused.

    proto_utils.uses_fast_cpp_protos_or_die()

    logging_level.set_from_flag()
    hts_verbose.set(hts_verbose.htsLogLevel[FLAGS.hts_logging_level])

    # Set up options; may do I/O.
    options = default_options(add_flags=True, flags_obj=FLAGS)
    check_options_are_valid(options)

    # Run!
    make_examples_core.make_examples_runner(options)


if __name__ == '__main__':
  flags.mark_flags_as_required([
      'examples',
      'mode',
      'reads',
      'ref',
  ])
  app.run(main)