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feat: add k-mer-seeded top-k ungapped local alignment #31

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feat: add k-mer-seeded top-k ungapped local alignment #31

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2 changes: 2 additions & 0 deletions seq_smith/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
overlap_align,
overlap_align_many,
top_k_ungapped_local_align,
top_k_ungapped_local_align_kmer,
top_k_ungapped_local_align_many,
)
from .python_utils import decode, encode, format_alignment_ascii, generate_cigar, make_score_matrix
Expand All @@ -33,5 +34,6 @@
"overlap_align",
"overlap_align_many",
"top_k_ungapped_local_align",
"top_k_ungapped_local_align_kmer",
"top_k_ungapped_local_align_many",
]
10 changes: 10 additions & 0 deletions seq_smith/_seq_smith.pyi
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Expand Up @@ -125,6 +125,16 @@ def top_k_ungapped_local_align(
filter_overlap_a: bool = True,
filter_overlap_b: bool = True,
) -> list[Alignment]: ...
def top_k_ungapped_local_align_kmer(
seqa: bytes,
seqb: bytes,
score_matrix: npt.NDArray[np.int32],
k: int,
kmer_size: int,
max_hits_per_kmer: int,
filter_overlap_a: bool = True,
filter_overlap_b: bool = True,
) -> list[Alignment]: ...
def top_k_ungapped_local_align_many(
seqa: bytes,
seqbs: Sequence[bytes],
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