svphaser 2.0.6__tar.gz → 2.1.0__tar.gz

svphaser-2.1.0/PKG-INFO

@@ -0,0 +1,231 @@
+Metadata-Version: 2.4
+Name: svphaser
+Version: 2.1.0
+Summary: Structural-variant phasing from HP-tagged long-read BAMs
+Project-URL: Homepage, https://github.com/SFGLab/SvPhaser
+Project-URL: Issues, https://github.com/SFGLab/SvPhaser/issues
+Project-URL: Source, https://github.com/SFGLab/SvPhaser
+Author-email: SvPhaser Team <you@lab.org>
+License: MIT
+License-File: LICENSE
+Keywords: BAM,ONT,VCF,genomics,long-reads,phasing,structural-variants
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Requires-Dist: cyvcf2>=0.30
+Requires-Dist: pandas>=2.1
+Requires-Dist: pysam>=0.23
+Requires-Dist: typer>=0.14
+Provides-Extra: bench
+Requires-Dist: py-spy>=0.3; extra == 'bench'
+Requires-Dist: pytest-benchmark>=4.0; extra == 'bench'
+Provides-Extra: dev
+Requires-Dist: black>=24.3; extra == 'dev'
+Requires-Dist: build>=1.2; extra == 'dev'
+Requires-Dist: hypothesis>=6.90; extra == 'dev'
+Requires-Dist: mypy>=1.8; extra == 'dev'
+Requires-Dist: pandas-stubs>=2.0; extra == 'dev'
+Requires-Dist: pre-commit>=3.6; extra == 'dev'
+Requires-Dist: pytest-cov>=5; extra == 'dev'
+Requires-Dist: pytest-xdist>=3.5; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Requires-Dist: ruff>=0.5; extra == 'dev'
+Requires-Dist: tox>=4.10; extra == 'dev'
+Requires-Dist: twine>=5.0; extra == 'dev'
+Provides-Extra: plots
+Requires-Dist: matplotlib>=3.7; extra == 'plots'
+Description-Content-Type: text/markdown
+
+# SvPhaser
+
+> **Haplotype-aware structural-variant (SV) genotyper for long-read data**
+
+[![PyPI version](https://img.shields.io/pypi/v/svphaser.svg?logo=pypi)](https://pypi.org/project/svphaser/)
+[![Python](https://img.shields.io/pypi/pyversions/svphaser.svg)](https://pypi.org/project/svphaser/)
+[![License](https://img.shields.io/github/license/SFGLab/SvPhaser.svg)](LICENSE)
+
+---
+
+**SvPhaser** phases **pre-called structural variants (SVs)** using **HP-tagged** long-read alignments (PacBio HiFi, ONT Q20+, …).
+
+Think of it as *WhatsHap* for insertions/deletions/duplications:
+- **we do not discover SVs**
+- **we assign haplotype genotypes** (`0|1`, `1|0`, `1|1`, or `./.`)
+- and compute a **Genotype Quality (GQ)** score
+
+All in a single, embarrassingly-parallel pass over the genome.
+
+## Highlights
+
+- **Fast per-chromosome multiprocessing** (scale-out on multi-core CPUs).
+- **Deterministic Δ-based decision logic** (no MCMC / HMM).
+- **CLI + Python API**.
+- **Non-destructive VCF augmentation**: injects phasing fields while preserving the original header and records.
+- **Configurable confidence bins** + optional plots.
+
+## Installation
+
+### From PyPI (recommended)
+
+```bash
+# Requires Python >= 3.9
+pip install svphaser
+````
+
+Optional extras (if you use them):
+
+```bash
+pip install "svphaser[plots]"
+pip install "svphaser[bench]"
+pip install "svphaser[dev]"
+```
+
+### From source
+
+```bash
+git clone https://github.com/SFGLab/SvPhaser.git
+cd SvPhaser
+pip install -e .
+```
+
+## Inputs & requirements
+
+SvPhaser expects:
+
+1. **Unphased SV VCF** (`.vcf` / `.vcf.gz`)
+
+   * SVs should already be called by your preferred SV caller.
+
+2. **HP-tagged BAM** (long-read alignments)
+
+   * Reads must contain haplotype tags (e.g., `HP`) produced by an upstream phasing pipeline.
+
+If your BAM is not HP-tagged, SvPhaser cannot assign haplotypes.
+
+## Quick start (CLI)
+
+```bash
+svphaser phase \
+    sample_unphased.vcf.gz \
+    sample.sorted_phased.bam \
+    --out-dir results/ \
+    --min-support 10 \
+    --major-delta 0.70 \
+    --equal-delta 0.25 \
+    --gq-bins "30:High,10:Moderate" \
+    --threads 32
+```
+
+### Outputs
+
+Inside `results/`:
+
+* `*_phased.vcf` — your original VCF with additional INFO fields:
+
+  * `HP_GT` — phased genotype
+  * `HP_GQ` — genotype quality score
+  * `HP_GQBIN` — confidence bin label (based on your `--gq-bins`)
+* `*_phased.csv` — tidy table for plotting / downstream analysis
+
+For algorithmic details, see: **`docs/methodology.md`**.
+
+## Python API
+
+```python
+from pathlib import Path
+from svphaser.phasing.io import phase_vcf
+
+phase_vcf(
+    Path("sample.vcf.gz"),
+    Path("sample.bam"),
+    out_dir=Path("results"),
+    min_support=10,
+    major_delta=0.70,
+    equal_delta=0.25,
+    gq_bins="30:High,10:Moderate",
+    threads=8,
+)
+```
+
+The phased table can also be loaded from the generated CSV for custom analytics.
+
+## Repository structure (high level)
+
+```
+SvPhaser/
+├─ src/svphaser/         # importable package
+├─ tests/                # test suite + small fixtures (if present)
+├─ docs/                 # methodology + notes
+├─ notebooks/            # experiments / analysis (if present)
+├─ figures/              # plots & diagrams (if present)
+├─ pyproject.toml
+└─ CHANGELOG.md
+```
+
+## Development
+
+```bash
+git clone https://github.com/SFGLab/SvPhaser.git
+cd SvPhaser
+
+python -m venv .venv
+source .venv/bin/activate
+
+pip install -e ".[dev]"
+pytest -q
+mypy src/svphaser
+```
+
+See `CONTRIBUTING.md` for contribution guidelines.
+
+## Citing SvPhaser
+
+If SvPhaser contributed to your research, please cite:
+
+```bibtex
+@software{svphaser2025,
+  author  = {Pranjul Mishra and Sachin Gadakh},
+  title   = {SvPhaser: Haplotype-aware structural-variant genotyping from HP-tagged long-read BAMs},
+  version = {2.0.6},
+  year    = {2025},
+  month   = nov,
+  url     = {https://github.com/SFGLab/SvPhaser},
+  note    = {PyPI: https://pypi.org/project/svphaser/}
+}
+```
+
+(If you need maximum rigor for a paper, cite a specific git commit hash too.)
+
+## License
+
+SvPhaser is released under the **MIT License** — see [LICENSE](LICENSE).
+
+## Contact
+
+Developed by **Team 5 (BioAI Hackathon)**.
+
+* Pranjul Mishra — [pranjul.mishra@proton.me](mailto:pranjul.mishra@proton.me)
+* Sachin Gadakh — [s.gadakh@cent.uw.edu.pl](mailto:s.gadakh@cent.uw.edu.pl)
+
+Issues and feature requests: please open a GitHub issue.
+
+```
+
+### Two hard notes (don’t ignore)
+- If you **don’t actually have CI set up**, don’t show a CI badge. A fake badge is worse than no badge.
+- If your repo layout doesn’t include `notebooks/figures/tests fixtures`, either adjust that tree block or remove it to avoid “template smell.”
+
+If you want, paste your **current `.github/workflows` filenames** (or tell me if you have none) and I’ll add the *correct* CI badge line too—without guessing.
+::contentReference[oaicite:1]{index=1}
+```
+
+[1]: https://pypi.org/project/svphaser/ "svphaser · PyPI"

svphaser-2.1.0/README.md

@@ -0,0 +1,184 @@
+# SvPhaser
+
+> **Haplotype-aware structural-variant (SV) genotyper for long-read data**
+
+[![PyPI version](https://img.shields.io/pypi/v/svphaser.svg?logo=pypi)](https://pypi.org/project/svphaser/)
+[![Python](https://img.shields.io/pypi/pyversions/svphaser.svg)](https://pypi.org/project/svphaser/)
+[![License](https://img.shields.io/github/license/SFGLab/SvPhaser.svg)](LICENSE)
+
+---
+
+**SvPhaser** phases **pre-called structural variants (SVs)** using **HP-tagged** long-read alignments (PacBio HiFi, ONT Q20+, …).
+
+Think of it as *WhatsHap* for insertions/deletions/duplications:
+- **we do not discover SVs**
+- **we assign haplotype genotypes** (`0|1`, `1|0`, `1|1`, or `./.`)
+- and compute a **Genotype Quality (GQ)** score
+
+All in a single, embarrassingly-parallel pass over the genome.
+
+## Highlights
+
+- **Fast per-chromosome multiprocessing** (scale-out on multi-core CPUs).
+- **Deterministic Δ-based decision logic** (no MCMC / HMM).
+- **CLI + Python API**.
+- **Non-destructive VCF augmentation**: injects phasing fields while preserving the original header and records.
+- **Configurable confidence bins** + optional plots.
+
+## Installation
+
+### From PyPI (recommended)
+
+```bash
+# Requires Python >= 3.9
+pip install svphaser
+````
+
+Optional extras (if you use them):
+
+```bash
+pip install "svphaser[plots]"
+pip install "svphaser[bench]"
+pip install "svphaser[dev]"
+```
+
+### From source
+
+```bash
+git clone https://github.com/SFGLab/SvPhaser.git
+cd SvPhaser
+pip install -e .
+```
+
+## Inputs & requirements
+
+SvPhaser expects:
+
+1. **Unphased SV VCF** (`.vcf` / `.vcf.gz`)
+
+   * SVs should already be called by your preferred SV caller.
+
+2. **HP-tagged BAM** (long-read alignments)
+
+   * Reads must contain haplotype tags (e.g., `HP`) produced by an upstream phasing pipeline.
+
+If your BAM is not HP-tagged, SvPhaser cannot assign haplotypes.
+
+## Quick start (CLI)
+
+```bash
+svphaser phase \
+    sample_unphased.vcf.gz \
+    sample.sorted_phased.bam \
+    --out-dir results/ \
+    --min-support 10 \
+    --major-delta 0.70 \
+    --equal-delta 0.25 \
+    --gq-bins "30:High,10:Moderate" \
+    --threads 32
+```
+
+### Outputs
+
+Inside `results/`:
+
+* `*_phased.vcf` — your original VCF with additional INFO fields:
+
+  * `HP_GT` — phased genotype
+  * `HP_GQ` — genotype quality score
+  * `HP_GQBIN` — confidence bin label (based on your `--gq-bins`)
+* `*_phased.csv` — tidy table for plotting / downstream analysis
+
+For algorithmic details, see: **`docs/methodology.md`**.
+
+## Python API
+
+```python
+from pathlib import Path
+from svphaser.phasing.io import phase_vcf
+
+phase_vcf(
+    Path("sample.vcf.gz"),
+    Path("sample.bam"),
+    out_dir=Path("results"),
+    min_support=10,
+    major_delta=0.70,
+    equal_delta=0.25,
+    gq_bins="30:High,10:Moderate",
+    threads=8,
+)
+```
+
+The phased table can also be loaded from the generated CSV for custom analytics.
+
+## Repository structure (high level)
+
+```
+SvPhaser/
+├─ src/svphaser/         # importable package
+├─ tests/                # test suite + small fixtures (if present)
+├─ docs/                 # methodology + notes
+├─ notebooks/            # experiments / analysis (if present)
+├─ figures/              # plots & diagrams (if present)
+├─ pyproject.toml
+└─ CHANGELOG.md
+```
+
+## Development
+
+```bash
+git clone https://github.com/SFGLab/SvPhaser.git
+cd SvPhaser
+
+python -m venv .venv
+source .venv/bin/activate
+
+pip install -e ".[dev]"
+pytest -q
+mypy src/svphaser
+```
+
+See `CONTRIBUTING.md` for contribution guidelines.
+
+## Citing SvPhaser
+
+If SvPhaser contributed to your research, please cite:
+
+```bibtex
+@software{svphaser2025,
+  author  = {Pranjul Mishra and Sachin Gadakh},
+  title   = {SvPhaser: Haplotype-aware structural-variant genotyping from HP-tagged long-read BAMs},
+  version = {2.0.6},
+  year    = {2025},
+  month   = nov,
+  url     = {https://github.com/SFGLab/SvPhaser},
+  note    = {PyPI: https://pypi.org/project/svphaser/}
+}
+```
+
+(If you need maximum rigor for a paper, cite a specific git commit hash too.)
+
+## License
+
+SvPhaser is released under the **MIT License** — see [LICENSE](LICENSE).
+
+## Contact
+
+Developed by **Team 5 (BioAI Hackathon)**.
+
+* Pranjul Mishra — [pranjul.mishra@proton.me](mailto:pranjul.mishra@proton.me)
+* Sachin Gadakh — [s.gadakh@cent.uw.edu.pl](mailto:s.gadakh@cent.uw.edu.pl)
+
+Issues and feature requests: please open a GitHub issue.
+
+```
+
+### Two hard notes (don’t ignore)
+- If you **don’t actually have CI set up**, don’t show a CI badge. A fake badge is worse than no badge.
+- If your repo layout doesn’t include `notebooks/figures/tests fixtures`, either adjust that tree block or remove it to avoid “template smell.”
+
+If you want, paste your **current `.github/workflows` filenames** (or tell me if you have none) and I’ll add the *correct* CI badge line too—without guessing.
+::contentReference[oaicite:1]{index=1}
+```
+
+[1]: https://pypi.org/project/svphaser/ "svphaser · PyPI"

{svphaser-2.0.6 → svphaser-2.1.0}/pyproject.toml

@@ -54,9 +54,9 @@ dev = [
 ]
 
 [project.urls]
-Homepage = "https://github.com/your-org/svphaser"
-Issues   = "https://github.com/your-org/svphaser/issues"
-Source   = "https://github.com/your-org/svphaser"
+Homepage = "https://github.com/SFGLab/SvPhaser"
+Issues   = "https://github.com/SFGLab/SvPhaser/issues"
+Source   = "https://github.com/SFGLab/SvPhaser"
 
 [project.scripts]
 svphaser = "svphaser.cli:app"
@@ -71,13 +71,23 @@ include = ["src/svphaser/py.typed"]
 [tool.hatch.build.targets.sdist]
 include = ["src/**", "README.md", "LICENSE", "pyproject.toml"]
 
-# Version from Git tags like v2.0.0 → 2.0.0
+# -------------------------------------------------------------------
+#  Versioning: hatch-vcs (tags like v2.0.8 -> 2.0.8)
+# -------------------------------------------------------------------
 [tool.hatch.version]
 source = "vcs"
+tag-pattern = "v(?P<version>.+)"
 
+# These are setuptools-scm options passed through hatch-vcs.
+# local_scheme removes "+g<hash>" which public indexes must not accept.
+# version_scheme avoids auto-bumping to the next patch on non-tag commits.
+[tool.hatch.version.raw-options]
+local_scheme = "no-local-version"
+version_scheme = "no-guess-dev"
+
+# Write resolved version to file at build time
 [tool.hatch.build.hooks.vcs]
 version-file = "src/svphaser/_version.py"
-tag-pattern = "v(?P<version>.+)"
 
 # -------------------------------------------------------------------
 #  Tooling (ruff / black / mypy / pytest / coverage)

{svphaser-2.0.6 → svphaser-2.1.0}/src/svphaser/__init__.py

@@ -1,7 +1,10 @@
 """Top-level SvPhaser package.
 
-Public surface kept tiny: a version string and a convenience helper
-that calls the library’s main phasing routine.
+Public surface kept tiny:
+- __version__
+- a convenience `phase()` wrapper around svphaser.phasing.io.phase_vcf()
+
+Defaults are chosen to match the recommended SvPhaser settings for long-read SV phasing.
 """
 
 from __future__ import annotations
@@ -11,7 +14,7 @@ from pathlib import Path
 # --------------------------------------------------------------------
 # Robust version lookup:
 # - Prefer installed package metadata (works for wheels and PEP 660 editables)
-# - Fall back to placeholder in _version.py for raw-source/dev use
+# - Fall back to _version.py for raw-source/dev use
 # --------------------------------------------------------------------
 try:
     from importlib.metadata import version as _pkg_version  # Python 3.8+
@@ -19,14 +22,14 @@ try:
     __version__ = _pkg_version("svphaser")
 except Exception:
     try:
-        from ._version import __version__  # "0+unknown" in repo; overwritten in builds
+        from ._version import __version__  # overwritten in builds when using setuptools-scm
     except Exception:  # highly defensive
         __version__ = "0+unknown"
 
 # Centralized defaults (keep CLI in sync)
 DEFAULT_MIN_SUPPORT: int = 10
-DEFAULT_MAJOR_DELTA: float = 0.70
-DEFAULT_EQUAL_DELTA: float = 0.25
+DEFAULT_MAJOR_DELTA: float = 0.60
+DEFAULT_EQUAL_DELTA: float = 0.10
 DEFAULT_GQ_BINS: str = "30:High,10:Moderate"
 
 
@@ -44,8 +47,10 @@ def phase(
 ) -> tuple[Path, Path]:
     """Phase *sv_vcf* using HP-tagged *bam*, writing outputs into *out_dir*.
 
-    Thin wrapper around :py:func:`svphaser.phasing.io.phase_vcf` so users/tests
-    can skip importing submodules.
+    Notes
+    -----
+    - Step B semantics: `min_support` is applied to TOTAL ALT-supporting reads (n1+n2).
+    - Near-ties (<= equal_delta) are treated as ambiguous (./.), not homozygous ALT.
 
     Returns
     -------
@@ -66,13 +71,13 @@ def phase(
     out_csv = out_dir_p / f"{stem}_phased.csv"
 
     phase_vcf(
-        sv_vcf,
-        bam,
-        out_dir=out_dir_p,  # type: ignore[arg-type]
+        Path(sv_vcf),
+        Path(bam),
+        out_dir=out_dir_p,
         min_support=min_support,
         major_delta=major_delta,
         equal_delta=equal_delta,
-        gq_bins=gq_bins,  # type: ignore[arg-type]
+        gq_bins=gq_bins,
         threads=threads,
     )
     return out_vcf, out_csv

{svphaser-2.0.6 → svphaser-2.1.0}/src/svphaser/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '2.0.6'
-__version_tuple__ = version_tuple = (2, 0, 6)
+__version__ = version = '2.1.0'
+__version_tuple__ = version_tuple = (2, 1, 0)
 
 __commit_id__ = commit_id = None

{svphaser-2.0.6 → svphaser-2.1.0}/src/svphaser/cli.py

@@ -1,14 +1,14 @@
 #!/usr/bin/env python3
-"""
-svphaser.cli
+"""svphaser.cli
 ============
 Command-line interface for **SvPhaser**.
 
 The program writes two files inside **--out-dir** (or the CWD):
 
-* ``<stem>_phased.vcf``   (uncompressed; GT/GQ and optional HP_GQBIN injected)
-* ``<stem>_phased.csv``   (tabular summary including gq_label column)
+* ``<stem>_phased.vcf``   (uncompressed; GT/GQ injected; optional INFO=GQBIN)
+* ``<stem>_phased.csv``   (tabular summary incl. n1/n2/gt/gq and optional gq_label)
 """
+
 from __future__ import annotations
 
 from pathlib import Path
@@ -27,7 +27,7 @@ from svphaser import (
 app = typer.Typer(add_completion=False, rich_markup_mode="rich")
 
 
-def _version_callback(value: bool):
+def _version_callback(value: bool) -> None:
     if value:
         typer.echo(__version__)
         raise typer.Exit()
@@ -44,30 +44,20 @@ def main(
             callback=_version_callback,
         ),
     ] = None
-):
+) -> None:
     """SvPhaser – Structural-variant phasing from HP-tagged long-read BAMs."""
-    # no-op; callback handles --version
     return
 
 
-# ──────────────────────────────────────────────────────────────────────────
-#  phase command
-# ──────────────────────────────────────────────────────────────────────────
 @app.command("phase")
 def phase_cmd(
     sv_vcf: Annotated[
         Path,
-        typer.Argument(
-            exists=True,
-            help="Input *un-phased* SV VCF (.vcf or .vcf.gz)",
-        ),
+        typer.Argument(exists=True, help="Input *un-phased* SV VCF (.vcf or .vcf.gz)"),
     ],
     bam: Annotated[
         Path,
-        typer.Argument(
-            exists=True,
-            help="Long-read BAM/CRAM with HP tags",
-        ),
+        typer.Argument(exists=True, help="Long-read BAM/CRAM with HP tags"),
     ],
     out_dir: Annotated[
         Path,
@@ -90,9 +80,8 @@ def phase_cmd(
         int,
         typer.Option(
             help=(
-                "Minimum HP-tagged reads per haplotype. "
-                "SVs where *both* n1 AND n2 fall below this "
-                "are dropped entirely."
+                "Minimum TOTAL ALT-supporting reads required to keep an SV (n1+n2). "
+                "If (n1+n2) < min_support the SV is dropped (written to *_dropped_svs.csv)."
             ),
             show_default=True,
         ),
@@ -100,14 +89,14 @@ def phase_cmd(
     major_delta: Annotated[
         float,
         typer.Option(
-            help="r >= this ⇒ strong majority ⇒ GT 1|0 or 0|1",
+            help="max(n1,n2)/N >= this ⇒ strong majority ⇒ GT 1|0 or 0|1",
             show_default=True,
         ),
     ] = DEFAULT_MAJOR_DELTA,
     equal_delta: Annotated[
         float,
         typer.Option(
-            help="|n1−n2|/N ≤ this ⇒ near-tie ⇒ GT 1|1",
+            help="|n1−n2|/N <= this ⇒ near-tie ⇒ GT ./. (ambiguous)",
             show_default=True,
         ),
     ] = DEFAULT_EQUAL_DELTA,
@@ -116,9 +105,8 @@ def phase_cmd(
         str,
         typer.Option(
             help=(
-                "Comma-separated GQ≥threshold:Label definitions "
-                "(e.g. '30:High,10:Moderate'). Labels appear in the CSV "
-                "[gq_label] and in the VCF INFO field HP_GQBIN when set."
+                "Comma-separated GQ≥threshold:Label definitions (e.g. '30:High,10:Moderate'). "
+                "Labels appear in CSV column [gq_label] and in the VCF INFO field GQBIN."
             ),
             show_default=True,
         ),
@@ -134,13 +122,11 @@ def phase_cmd(
         ),
     ] = None,
 ) -> None:
-    """Phase structural variants using HP-tagged read evidence."""
-    # Initialise logging BEFORE we import anything that might log
+    """Phase structural variants using SV-type-aware ALT-support evidence."""
     from svphaser.logging import init as _init_logging
 
-    _init_logging("INFO")  # or "DEBUG" if you want more detail
+    _init_logging("INFO")
 
-    # Resolve output paths
     if not out_dir.exists():
         out_dir.mkdir(parents=True)
 
@@ -153,25 +139,21 @@ def phase_cmd(
     out_vcf = out_dir / f"{stem}_phased.vcf"
     out_csv = out_dir / f"{stem}_phased.csv"
 
-    # Lazy import so `svphaser --help` works without heavy deps
     from svphaser.phasing.io import phase_vcf
 
     try:
         phase_vcf(
             sv_vcf,
             bam,
-            out_dir=out_dir,  # type: ignore[arg-type]
+            out_dir=out_dir,
             min_support=min_support,
             major_delta=major_delta,
             equal_delta=equal_delta,
-            gq_bins=gq_bins,  # type: ignore[arg-type]
+            gq_bins=gq_bins,
             threads=threads,
         )
         typer.secho(f"✔ Phased VCF → {out_vcf}", fg=typer.colors.GREEN)
         typer.secho(f"✔ Phased CSV → {out_csv}", fg=typer.colors.GREEN)
-    except Exception:  # pragma: no cover
-        typer.secho(
-            "[SvPhaser] 💥  Unhandled error during phasing",
-            fg=typer.colors.RED,
-        )
+    except Exception:
+        typer.secho("[SvPhaser] 💥  Unhandled error during phasing", fg=typer.colors.RED)
         raise