folded · folded · Dec 27, 2025 · Dec 27, 2025 · Dec 27, 2025 · Dec 27, 2025
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp310-cp310-macosx_10_12_x86_64.whl b/for_pypi_upload/seq_smith-0.1.0-cp310-cp310-macosx_10_12_x86_64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp310-cp310-macosx_11_0_arm64.whl b/for_pypi_upload/seq_smith-0.1.0-cp310-cp310-macosx_11_0_arm64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl b/for_pypi_upload/seq_smith-0.1.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/for_pypi_upload/seq_smith-0.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp310-cp310-win_amd64.whl b/for_pypi_upload/seq_smith-0.1.0-cp310-cp310-win_amd64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp311-cp311-macosx_10_12_x86_64.whl b/for_pypi_upload/seq_smith-0.1.0-cp311-cp311-macosx_10_12_x86_64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp311-cp311-macosx_11_0_arm64.whl b/for_pypi_upload/seq_smith-0.1.0-cp311-cp311-macosx_11_0_arm64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl b/for_pypi_upload/seq_smith-0.1.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/for_pypi_upload/seq_smith-0.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp311-cp311-win_amd64.whl b/for_pypi_upload/seq_smith-0.1.0-cp311-cp311-win_amd64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp312-cp312-macosx_10_13_x86_64.whl b/for_pypi_upload/seq_smith-0.1.0-cp312-cp312-macosx_10_13_x86_64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp312-cp312-macosx_11_0_arm64.whl b/for_pypi_upload/seq_smith-0.1.0-cp312-cp312-macosx_11_0_arm64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl b/for_pypi_upload/seq_smith-0.1.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/for_pypi_upload/seq_smith-0.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp312-cp312-win_amd64.whl b/for_pypi_upload/seq_smith-0.1.0-cp312-cp312-win_amd64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp313-cp313-macosx_10_13_x86_64.whl b/for_pypi_upload/seq_smith-0.1.0-cp313-cp313-macosx_10_13_x86_64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp313-cp313-macosx_11_0_arm64.whl b/for_pypi_upload/seq_smith-0.1.0-cp313-cp313-macosx_11_0_arm64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl b/for_pypi_upload/seq_smith-0.1.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/for_pypi_upload/seq_smith-0.1.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0-cp313-cp313-win_amd64.whl b/for_pypi_upload/seq_smith-0.1.0-cp313-cp313-win_amd64.whl
diff --git a/for_pypi_upload/seq_smith-0.1.0.tar.gz b/for_pypi_upload/seq_smith-0.1.0.tar.gz
diff --git a/seq_smith/__init__.py b/seq_smith/__init__.py
@@ -10,6 +10,8 @@
     local_global_align_many,
     overlap_align,
     overlap_align_many,
+    top_k_ungapped_local_align,
+    top_k_ungapped_local_align_many,
 )
 from .python_utils import decode, encode, format_alignment_ascii, generate_cigar, make_score_matrix
 
@@ -30,4 +32,6 @@
     "make_score_matrix",
     "overlap_align",
     "overlap_align_many",
+    "top_k_ungapped_local_align",
+    "top_k_ungapped_local_align_many",
 ]
diff --git a/seq_smith/_seq_smith.pyi b/seq_smith/_seq_smith.pyi
@@ -117,3 +117,20 @@ def overlap_align_many(
     gap_extend: int,
     num_threads: int | None = None,
 ) -> list[Alignment]: ...
+def top_k_ungapped_local_align(
+    seqa: bytes,
+    seqb: bytes,
+    score_matrix: npt.NDArray[np.int32],
+    k: 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],
+    score_matrix: npt.NDArray[np.int32],
+    k: int,
+    num_threads: int | None = None,
+    filter_overlap_a: bool = True,
+    filter_overlap_b: bool = True,
+) -> list[list[Alignment]]: ...