from typing import List, Dict, Tuple

blast_index_location_type = Tuple[str, bool, int]
"""
Type of a location. Will cost 64 bytes.

[chromosome_name, strand, offset]

strand is True for default and False for reverse complementary strand.
"""

blast_index_locations_type = List[blast_index_location_type]
"""
The values of `blast_simple_index_type`. Should be a list of `blast_index_location_type`
"""

blast_simple_index_type = Dict[bytes, blast_index_locations_type]
"""
The type of blast index. Will be a Dictionary with:

index_item -> blast_index_locations_type
"""

blast_indices_type = Dict[bytes, blast_simple_index_type]
"""
Indexed using prefix to save memory.
"""

DEFAULT_WORD_LEN = 11
DEFAULT_CHUNK_LEN = 2000000
DEFAULT_PREFIX_LEN = 3
DEFAULT_SCORE_CUTOFF_SLOPE = 1.5
DEFAULT_SCORE_CUTOFF_INTERSECT = 0.0
DEFAULT_EXTENDER_BATCH_SIZE = 200

from herv_finder.blast._cblast import *

from typing import List, Dict, Tuple

blast_index_location_type = Tuple[str, bool, int]
"""
Type of a location. Will cost 64 bytes.

[chromosome_name, strand, offset]

strand is True for default and False for reverse complementary strand.
"""

blast_index_locations_type = List[blast_index_location_type]
"""
The values of `blast_simple_index_type`. Should be a list of `blast_index_location_type`
"""

blast_simple_index_type = Dict[bytes, blast_index_locations_type]
"""
The type of blast index. Will be a Dictionary with:

index_item -> blast_index_locations_type
"""

blast_indices_type = Dict[bytes, blast_simple_index_type]
"""
Indexed using prefix to save memory.
"""

DEFAULT_WORD_LEN = 11
DEFAULT_CHUNK_LEN = 2000000
DEFAULT_PREFIX_LEN = 3
DEFAULT_SCORE_CUTOFF_SLOPE = 1.5
DEFAULT_SCORE_CUTOFF_INTERSECT = 0.0
DEFAULT_EXTENDER_BATCH_SIZE = 200

from herv_finder.blast._cblast import *

Type of a location. Will cost 64 bytes.  [chromosome_name, strand, offset]  strand is True for default and False for reverse complementary strand. The values of `blast_simple_index_type`. Should be a list of `blast_index_location_type` The type of blast index. Will be a Dictionary with:  index_item -> blast_index_locations_type Indexed using prefix to save memory.