scanitd 0.9.2__tar.gz → 0.9.3__tar.gz

scanitd-0.9.3/.github/workflows/release.yml

@@ -0,0 +1,88 @@
+name: Release to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  test:
+    name: Run test suite
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Install dependencies
+        run: uv sync --group dev
+
+      - name: Run tests
+        run: uv run pytest
+
+  build_sdist:
+    name: Build source distribution
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Build sdist
+        run: uv build --sdist
+
+      - name: Upload sdist artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: pypi-sdist
+          path: dist/
+
+  build_wheels:
+    name: Build wheels (${{ matrix.os }})
+    needs: test
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels with cibuildwheel
+        uses: pypa/cibuildwheel@v4.3.5
+        with:
+          output-dir: dist
+
+      - name: Upload wheel artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: pypi-wheels-${{ matrix.os }}
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: [build_sdist, build_wheels]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/scanitd
+    permissions:
+      id-token: write
+    steps:
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: pypi-sdist
+          path: dist/
+
+      - name: Download wheel artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: pypi-wheels-*
+          path: dist/
+          merge-multiple: true
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

{scanitd-0.9.2 → scanitd-0.9.3}/.gitignore

@@ -3,8 +3,9 @@ __pycache__/
 *.py[cod]
 *$py.class
 
-# C extensions
+# C extensions and object files
 *.so
+*.o
 
 # Distribution / packaging
 .Python
@@ -116,4 +117,6 @@ ENV/
 # Tool configurations
 .omc/
 .serena/
+BIOCONDA.md
+CLAUDE.md
 

{scanitd-0.9.2 → scanitd-0.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: scanitd
-Version: 0.9.2
+Version: 0.9.3
 Summary: ScanITD
 Project-URL: Homepage, https://github.com/ylab-hi/ScanITD
 Project-URL: Repository, https://github.com/ylab-hi/ScanITD
@@ -22,7 +22,6 @@ Requires-Dist: psutil>=5.9.5
 Requires-Dist: pyfaidx>=0.7.2
 Requires-Dist: pysam>=0.22.0
 Requires-Dist: rich>=13.7.0
-Requires-Dist: ssw-py>=1.0.1
 Requires-Dist: typer>=0.12.5
 Provides-Extra: docs
 Requires-Dist: myst-parser==3.0.0; extra == 'docs'
@@ -35,15 +34,33 @@ Description-Content-Type: text/markdown
 # ScanITD
 
 [![PyPI version](https://img.shields.io/pypi/v/scanitd.svg)](https://pypi.python.org/pypi/scanitd)
-[![PyPI - Wheel](https://img.shields.io/pypi/wheel/scanitd)](https://pypi.org/project/scanitd/#files)
+[![Conda Version](https://img.shields.io/conda/vn/bioconda/scanitd.svg)](https://anaconda.org/bioconda/scanitd)
+[![PyPI - Wheel](https://img.shields.io/pypi/wheel/scanitd)](https://pypi.python.org/pypi/scanitd/#files)
 [![license](https://img.shields.io/pypi/l/scanitd.svg)](https://github.com/ylab-hi/ScanITD/blob/main/LICENSE)
 [![Documentation Status](https://readthedocs.org/projects/scanitd/badge/?version=latest)](https://scanitd.readthedocs.io)
 
 
 # 📦 Installation
 
-ScanITD can be installed using pip, the Python package installer.
-Follow these steps to install:
+ScanITD can be installed using **Conda** (via the Bioconda channel) or **pip**.
+
+### Via Conda (Bioconda)
+
+To install ScanITD using Conda:
+
+```bash
+conda install -c bioconda scanitd
+```
+
+Or using the modern `bioconda::scanitd` specifier:
+
+```bash
+conda install bioconda::scanitd
+```
+
+### Via Pip
+
+ScanITD can also be installed using pip, the Python package installer:
 
 1. Ensure you have Python 3.10 or later installed on your system.
 
@@ -60,11 +77,13 @@ Follow these steps to install:
    pip install scanitd
    ```
 
-4. Verify the installation:
+### Verification
 
-   ```bash
-   scanitd --help
-   ```
+Verify the installation:
+
+```bash
+scanitd --help
+```
 
 # 🛠️ Usage
 

{scanitd-0.9.2 → scanitd-0.9.3}/README.md

@@ -1,15 +1,33 @@
 # ScanITD
 
 [![PyPI version](https://img.shields.io/pypi/v/scanitd.svg)](https://pypi.python.org/pypi/scanitd)
-[![PyPI - Wheel](https://img.shields.io/pypi/wheel/scanitd)](https://pypi.org/project/scanitd/#files)
+[![Conda Version](https://img.shields.io/conda/vn/bioconda/scanitd.svg)](https://anaconda.org/bioconda/scanitd)
+[![PyPI - Wheel](https://img.shields.io/pypi/wheel/scanitd)](https://pypi.python.org/pypi/scanitd/#files)
 [![license](https://img.shields.io/pypi/l/scanitd.svg)](https://github.com/ylab-hi/ScanITD/blob/main/LICENSE)
 [![Documentation Status](https://readthedocs.org/projects/scanitd/badge/?version=latest)](https://scanitd.readthedocs.io)
 
 
 # 📦 Installation
 
-ScanITD can be installed using pip, the Python package installer.
-Follow these steps to install:
+ScanITD can be installed using **Conda** (via the Bioconda channel) or **pip**.
+
+### Via Conda (Bioconda)
+
+To install ScanITD using Conda:
+
+```bash
+conda install -c bioconda scanitd
+```
+
+Or using the modern `bioconda::scanitd` specifier:
+
+```bash
+conda install bioconda::scanitd
+```
+
+### Via Pip
+
+ScanITD can also be installed using pip, the Python package installer:
 
 1. Ensure you have Python 3.10 or later installed on your system.
 
@@ -26,11 +44,13 @@ Follow these steps to install:
    pip install scanitd
    ```
 
-4. Verify the installation:
+### Verification
 
-   ```bash
-   scanitd --help
-   ```
+Verify the installation:
+
+```bash
+scanitd --help
+```
 
 # 🛠️ Usage
 

scanitd-0.9.3/conda/meta.yaml

@@ -0,0 +1,53 @@
+{% set name = "scanitd" %}
+{% set version = "0.9.3" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/scanitd-{{ version }}.tar.gz
+  sha256: 554efdf1c206a332fca1933a2ffb765d26127e22aaacadf86d170d21cbe288a6  # TODO: update sha256 after PyPI upload of 0.9.3
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('scanitd', max_pin="x.x") }}
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  entry_points:
+    - scanitd = scanitd.cli.cli:app
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - make
+  host:
+    - python >=3.9
+    - pip
+    - hatchling
+  run:
+    - python >=3.9
+    - numpy >=2.0.0
+    - pysam >=0.22.0
+    - pyfaidx >=0.7.2
+    - psutil >=5.9.5
+    - loguru >=0.7.0
+    - typer >=0.12.5
+    - rich >=13.7.0
+
+test:
+  commands:
+    - scanitd --help
+
+about:
+  home: https://github.com/ylab-hi/ScanITD
+  summary: Detecting internal tandem duplication with robust variant allele frequency estimation
+  license: MIT
+  license_file: LICENSE
+  doc_url: https://scanitd.readthedocs.io
+
+extra:
+  identifiers:
+    - doi:10.1093/gigascience/giaa089
+  recipe-maintainers:
+    - dolittle007

scanitd-0.9.3/docs/source/changelog.md

@@ -0,0 +1,81 @@
+# Changelog
+
+All notable changes to ScanITD will be documented in this file.
+
+The format follows [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and the project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+---
+
+## [0.9.3] — 2026-11-13
+
+### Fixed
+- Removed the 8,000x `pysam.pileup()` depth cap that caused AF underestimation on deep amplicon data (now uncapped by default via `2**31 - 1`, configurable with `--max-depth`)
+- Converted 0-based BED start coordinates (`start + 1`) to 1-based samtools region strings in `parse_target_genomic_coordinates()`, preventing `ValueError: start out of range (-1)` when a BED interval starts at `0`
+
+### Changed
+- Vendored the MIT-licensed Striped Smith-Waterman (SSW) C library and `ctypes` Python wrapper under `src/scanitd/ssw`, removing the external `ssw-py` dependency
+- Added a Hatchling custom build hook (`src/scanitd/ssw/build_ssw.py`) to compile `ssw.so` from source during wheel builds (with `sse2neon.h` support for ARM64)
+- Updated `conda/meta.yaml` for native C extension builds (`{{ compiler('c') }}`, `make`) and removed `ssw-py`
+
+### Added
+- Unit tests for `scanitd.ssw.AlignmentMgr` and `Alignment` (`tests/test_ssw.py`)
+- Unit and end-to-end split-read rescue tests for `scanitd.inference.sr_resuer` (`tests/test_sr_resuer.py`)
+
+---
+
+## [0.9.2] — 2026-07-16
+
+### Fixed
+- Filtering options were not applied (#11)
+- Potential error in `inference/main.py` (#10)
+- Various bug fixes across the `base`, `inference`, and `writer` modules
+
+### Changed
+- Releases now publish to PyPI via GitHub Actions using
+  [PyPI trusted publishing](https://docs.pypi.org/trusted-publishers/) (OIDC),
+  replacing manual `twine upload`
+- Removed `poetry.lock` in favor of a single `pyproject.toml`/`uv.lock`-based
+  dependency setup
+- Updated Python version requirements and dependencies
+- Bumped dev dependencies: `pip` (19.2.3 → 26.1), `wheel` (0.33.6 → 0.38.1)
+
+### Added
+- Comprehensive test suite
+
+---
+
+## [0.9.1] — 2024-11-20
+
+### Added
+- Full Google-style docstrings across all modules (`base`, `inference`, `writer`, `cli`)
+- Sphinx documentation with `autodoc`, `napoleon`, `sphinx-click`, and RTD theme
+- User guide pages: Installation, Quick Start, Usage, Output format
+- `sphinx-rtd-theme` and `sphinx-click` added to dev dependencies
+
+### Changed
+- Dev dependency group reduced from 38 to 19 packages by removing redundant
+  flake8 ecosystem (replaced by ruff), `black`, `isort`, `reorder-python-imports`,
+  `pynvim`, `cohesion`, `nox`, `xdoctest`, and `safety`
+- `[tool.isort]` config section removed from `pyproject.toml`
+
+---
+
+## [0.9.0] — 2024-11-08
+
+### Added
+- Initial public release of ScanITD 2.0
+- Chimeric-read (SA-tag) based TDUP detection
+- Large-insertion (CIGAR-I) based TDUP/INS detection
+- Split-read rescue via Smith-Waterman alignment (ssw-py)
+- VCF 4.3 output with `OAO`, `AO`, `AF`, `INSSEQ`, `HOMSEQ` INFO fields
+- Typer-based CLI with `--target` BED/region support
+- Loguru-based structured logging
+
+---
+
+## Citation
+
+Wang TY. and Yang R. [ScanITD: Detecting internal tandem duplication with robust
+variant allele frequency estimation](https://doi.org/10.1093/gigascience/giaa089).
+*GigaScience*, 2020.

{scanitd-0.9.2 → scanitd-0.9.3}/docs/source/conf.py

@@ -13,7 +13,7 @@ sys.path.insert(0, str(Path(__file__).resolve().parents[2] / "src"))
 project = "ScanITD"
 copyright = "2024, Ting-You Wang"
 author = "Ting-You Wang"
-release = "0.9.1"
+release = "0.9.3"
 version = "0.9"
 
 # -- General configuration ---------------------------------------------------

{scanitd-0.9.2 → scanitd-0.9.3}/docs/source/guide/usage.md

@@ -32,6 +32,7 @@ file and writes results in VCF 4.3 format.
 | `--depth` | `-d` | `10` | Minimum read depth at the locus |
 | `--vaf` | `-f` | `0.1` | Minimum variant allele frequency (0–1) |
 | `--length` | | `10` | Minimum ITD length in base pairs |
+| `--max-depth` | | `0` | Maximum pileup read depth per position (`0` for unlimited) |
 
 ### Alignment sensitivity
 
@@ -78,7 +79,7 @@ insertions (INS).
 ### 3. Soft-clipped read rescue
 
 Soft-clipped reads that lack an SA tag are aligned against the expected
-duplicated reference sequence using Smith-Waterman alignment (ssw-py). Those
+duplicated reference sequence using the vendored Smith-Waterman library (`scanitd.ssw`). Those
 whose alignment is end-anchored and passes the mismatch threshold are counted
 as additional supporting reads, improving VAF estimates.
 

{scanitd-0.9.2 → scanitd-0.9.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "scanitd"
-version = "0.9.2"
+version = "0.9.3"
 description = "ScanITD"
 authors = [
     { name = "Ting-You Wang", email = "tywang@northwestern.edu" },
@@ -21,7 +21,7 @@ dependencies = [
     "pysam>=0.22.0",
     "pyfaidx>=0.7.2",
     "psutil>=5.9.5",
-    "ssw-py>=1.0.1",
+    # ssw-py is vendored directly under src/scanitd/ssw
     "loguru>=0.7.0",
     "typer>=0.12.5",
     "rich>=13.7.0",
@@ -74,6 +74,17 @@ build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/scanitd"]
+exclude = ["*.o"]
+
+[tool.hatch.build.hooks.custom]
+path = "src/scanitd/ssw/build_ssw.py"
+
+
+[tool.cibuildwheel]
+build = ["cp310-*", "cp311-*", "cp312-*", "cp313-*"]
+skip = ["*-musllinux*", "*_i686"]
+test-command = "scanitd --version && python -c \"from scanitd.ssw import AlignmentMgr; m = AlignmentMgr(); m.set_read('ACGT'); m.set_reference('TTACGTTT'); r = m.align(); assert r.CIGAR == '4M' and r.reference_start == 2\""
+
 
 [tool.uv]
 package = true

{scanitd-0.9.2 → scanitd-0.9.3}/src/scanitd/__init__.py

@@ -1,5 +1,5 @@
 """Top-level package for ScanITD."""
 
 __author__ = """Ting-You Wang"""
-__version__ = "0.9.2"
+__version__ = "0.9.3"
 __PACKAGE_NAME__ = "ScanITD"

{scanitd-0.9.2 → scanitd-0.9.3}/src/scanitd/cli/cli.py

@@ -19,6 +19,14 @@ def itd_len_type(value: int) -> int:
     return int(value)
 
 
+def max_depth_type(value: int) -> int:
+    """Validate that max pileup depth is non-negative."""
+    if int(value) < 0:
+        msg = "max-depth must be non-negative (0 for unlimited)"
+        raise typer.BadParameter(msg)
+    return int(value)
+
+
 def version_callback(value: bool):
     """Print the ScanITD version string and exit.
 
@@ -119,6 +127,12 @@ def main(
         "--target",
         help="Limit analysis to targets listed in the BED-format file or a samtools region string",
     ),
+    max_depth: int = typer.Option(
+        0,
+        "--max-depth",
+        callback=max_depth_type,
+        help="Maximum pileup read depth per position (0 for unlimited)",
+    ),
     log_level: LogLevel = typer.Option(LogLevel.INFO, "-l", "--log-level", help="set the logging level."),
     version: bool | None = typer.Option(
         None,
@@ -143,6 +157,7 @@ def main(
         mismatch_sr: Maximum mismatches for soft-read rescue alignment (default: 1).
         mismatch_insertion: Maximum mismatches for insertion-inferred duplication (default: 2).
         target: BED file path or samtools region string to restrict analysis.
+        max_depth: Maximum pileup read depth per position; 0 means unlimited (default: 0).
         log_level: Logging verbosity level (default: INFO).
         version: When provided, prints version and exits.
     """
@@ -165,6 +180,7 @@ def main(
         allowed_mismatches_for_sr_rescue=mismatch_sr,
         allowed_mismatches_for_insertion=mismatch_insertion,
         logger=logger,
+        max_depth=max_depth,
     )
 
     write_events_to_vcf(output, bam_header, event_list, logger, min_ao=ao, min_depth=dp, min_vaf=vaf)

{scanitd-0.9.2 → scanitd-0.9.3}/src/scanitd/inference/helper.py

@@ -352,11 +352,16 @@ def parse_target_genomic_coordinates(input_data):
         return result
 
     # Helper function to validate and convert coordinates
-    def validate_coordinates(chrom, start, end):
+    def validate_coordinates(chrom, start, end, *, is_bed: bool = False):
         try:
             start = int(start)
             end = int(end)
-            if start < 0 or end < 0 or start >= end:
+            if is_bed:
+                # BED is 0-based half-open [start, end); convert to 1-based inclusive chrom:start-end
+                if start < 0 or end < 0 or start >= end:
+                    raise ValueError
+                return f"{chrom}:{start + 1}-{end}"
+            if start < 1 or end < 1 or start > end:
                 raise ValueError
             return f"{chrom}:{start}-{end}"
         except ValueError:
@@ -374,7 +379,7 @@ def parse_target_genomic_coordinates(input_data):
                 if line.strip() and not line.startswith("#"):
                     fields = line.strip().split("\t")
                     if len(fields) >= 3:
-                        result.append(validate_coordinates(fields[0], fields[1], fields[2]))
+                        result.append(validate_coordinates(fields[0], fields[1], fields[2], is_bed=True))
                     else:
                         msg = f"Invalid BED format in line: {line}"
                         raise ValueError(msg)
@@ -396,7 +401,7 @@ def parse_target_genomic_coordinates(input_data):
             try:
                 chrom, pos = entry.split(":")
                 start, end = pos.split("-")
-                result.append(validate_coordinates(chrom, start, end))
+                result.append(validate_coordinates(chrom, start, end, is_bed=False))
             except ValueError:
                 msg = f"Invalid chrom:start-end format: {entry}"
                 raise ValueError(msg)
@@ -405,7 +410,7 @@ def parse_target_genomic_coordinates(input_data):
         elif "\t" in entry:
             fields = entry.split("\t")
             if len(fields) >= 3:
-                result.append(validate_coordinates(fields[0], fields[1], fields[2]))
+                result.append(validate_coordinates(fields[0], fields[1], fields[2], is_bed=True))
             else:
                 msg = f"Invalid BED format: {entry}"
                 raise ValueError(msg)

{scanitd-0.9.2 → scanitd-0.9.3}/src/scanitd/inference/main.py

@@ -227,6 +227,9 @@ class BamScanner:
         return self.tdup_anchors
 
 
+_PYSAM_UNLIMITED_DEPTH = 2**31 - 1
+
+
 def scan_itd(
     in_bam_path,
     mapq_cutoff,
@@ -237,6 +240,7 @@ def scan_itd(
     allowed_mismatches_for_insertion,
     logger,
     microinsertion_cutoff: int = 10,
+    max_depth: int = 0,
 ):
     """Run the full ScanITD detection pipeline on a BAM file.
 
@@ -258,12 +262,19 @@ def scan_itd(
         logger: Logger instance implementing LoggerType.
         microinsertion_cutoff: Maximum microinsertion length at a breakpoint
             (default: 10).
+        max_depth: Maximum pileup read depth per position; 0 means unlimited
+            (default: 0).
 
     Returns:
         tuple: A 2-tuple of (sorted_event_list, bam_header) where sorted_event_list
             is a list of :class:`~scanitd.base.Event` objects sorted by (chrom, ref_start)
             and bam_header is the raw BAM header dict.
     """
+    if max_depth < 0:
+        msg = f"max_depth must be non-negative, got {max_depth}"
+        raise ValueError(msg)
+    effective_max_depth = _PYSAM_UNLIMITED_DEPTH if max_depth == 0 else max_depth
+
     regions = parse_target_genomic_coordinates(target_file)
 
     if len(regions) == 0:
@@ -297,7 +308,7 @@ def scan_itd(
 
     for _region in regions:
         try:
-            for pileup_column in bam_object.pileup(region=_region, stepper="all", truncate=True):
+            for pileup_column in bam_object.pileup(region=_region, stepper="all", truncate=True, max_depth=effective_max_depth):
                 # a list of pysam.PileupRead
                 for pileup_read in pileup_column.pileups:
                     position_of_pileup_site = pileup_read.query_position

{scanitd-0.9.2 → scanitd-0.9.3}/src/scanitd/inference/sr_resuer.py

@@ -1,6 +1,6 @@
 """Split-read rescue functions for augmenting tandem duplication allele observations.
 
-Uses Smith-Waterman local alignment (ssw-py) to rescue soft-clipped reads
+Uses vendored Smith-Waterman local alignment (scanitd.ssw) to rescue soft-clipped reads
 that support a TDUP event but lack an SA tag, improving allele frequency estimates.
 """
 
@@ -8,20 +8,21 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING
 
-from ssw import AlignmentMgr
-
 from scanitd.base import MappingMode
+from scanitd.ssw import AlignmentMgr
 
 if TYPE_CHECKING:
     from pyfaidx import Fasta
 
+    from scanitd.base import MicroRegion
+
 __all__ = [
     "update_tdup_ao",
 ]
 
 
 def update_tdup_ao(
-    tdup_id: tuple[str, int, int, str],
+    tdup_id: tuple[str, int, int, str, MicroRegion],
     original_ao: int,
     genome_fasta: Fasta,
     to_be_rescued_sequences: dict,

scanitd-0.9.3/src/scanitd/ssw/LICENSE-ssw-py.txt

@@ -0,0 +1,58 @@
+## ssw-py wrapper and utilities
+
+Copyright (C) 2017 Wyss Institute at Harvard University
+Copyright (C) 2023 Nick Conway
+
+The MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+http://www.opensource.org/licenses/mit-license.php
+
+## Complete-Striped-Smith-Waterman-Library (SSW C implementation)
+https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
+
+License: MIT
+
+Copyright (c) 2012-2015 Boston College
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+Author:
+C implementation: Mengyao Zhao
+
+## sse2neon.h (ARM64 NEON translation header)
+https://github.com/DLTcollab/sse2neon
+License: MIT

scanitd-0.9.3/src/scanitd/ssw/Makefile

@@ -0,0 +1,17 @@
+CC ?= gcc
+CFLAGS = -O3 -fPIC -std=c99 -Wall -Wextra -I. $(ARCHFLAGS)
+LDFLAGS = -lm
+SRC = ssw.c str_util.c
+OBJ = $(SRC:.c=.o)
+TARGET = ssw.so
+
+all: $(TARGET)
+
+$(TARGET): $(OBJ)
+	$(CC) $(ARCHFLAGS) -shared -o $@ $^ $(LDFLAGS)
+
+%.o: %.c ssw.h str_util.h
+	$(CC) $(CFLAGS) -c $< -o $@
+
+clean:
+	rm -f $(OBJ) $(TARGET)