LOPHOS v0.1.1: lint & typing clean; ready for data runs

Author: PM-0125

pyproject.toml

@@ -51,11 +51,12 @@ lint.ignore = ["E501"]  # handled by black
 
 [tool.mypy]
 python_version = "3.10"
+ignore_missing_imports = true
 warn_unused_ignores = true
 warn_redundant_casts = true
 strict = true
 exclude = ["tests/"]
-ignore_missing_imports = true
+
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/lophos"]

src/lophos/__main__.py

@@ -1,2 +1,3 @@
 from .cli import app
+
 app()

src/lophos/__pycache__/__init__.cpython-310.pyc

@@ -15,10 +15,12 @@
 app = typer.Typer(no_args_is_help=True, add_completion=False)
 console = Console()
 
+
 @app.callback()
 def main() -> None:
     """LOPHOS — Allele-specific phasing of CTCF peaks & loops from phased HiChIP BAMs."""
 
+
 @app.command("phase")
 def phase(
     bam: Annotated[Path, typer.Option(exists=True, help="Phased HiChIP BAM with RG tags")],
@@ -27,13 +29,17 @@ def phase(
     out: Annotated[Path, typer.Option(help="Output prefix (directory will be created)")],
     mapq: Annotated[int, typer.Option(help="Minimum MAPQ to count")] = 30,
     peak_window: Annotated[int, typer.Option(help="Peak summit +/- bp window")] = 500,
-    anchor_pad: Annotated[int, typer.Option(help="Anchor padding (bp) when matching mates")] = 10_000,
+    anchor_pad: Annotated[
+        int, typer.Option(help="Anchor padding (bp) when matching mates")
+    ] = 10_000,
     min_reads_peak: Annotated[int, typer.Option(help="Min total reads to call a peak")] = 5,
     min_pairs_loop: Annotated[int, typer.Option(help="Min informative pairs to call a loop")] = 3,
     fdr: Annotated[float, typer.Option(help="BH-FDR threshold")] = 0.05,
     keep_duplicates: Annotated[bool, typer.Option(help="Keep PCR/optical duplicates")] = False,
     validate_loops: Annotated[str, typer.Option(help="{none,local} (advanced later)")] = "local",
-    config: Annotated[Path | None, typer.Option(help="YAML config to override/record params")] = None,
+    config: Annotated[
+        Path | None, typer.Option(help="YAML config to override/record params")
+    ] = None,
 ) -> None:
     """Phase CTCF peaks and loops using a haplotype-tagged BAM."""
     if config:
@@ -51,16 +57,21 @@ def phase(
         bam=bam_handle, peaks=peaks_df, mapq=mapq, window_bp=peak_window, keep_dups=keep_duplicates
     )
     peak_stats = stats.compute_peak_stats(peak_counts)
-    peak_calls = calls.call_bias_for_peaks(peak_stats, thresholds=BiasThresholds(min_reads=min_reads_peak, fdr=fdr))
+    peak_calls = calls.call_bias_for_peaks(
+        peak_stats, thresholds=BiasThresholds(min_reads=min_reads_peak, fdr=fdr)
+    )
 
     loop_counts = counts_loops.count_loops(
         bam=bam_handle, loops=loops_df, mapq=mapq, anchor_pad=anchor_pad, keep_dups=keep_duplicates
     )
     loop_stats = stats.compute_loop_stats(loop_counts)
-    loop_calls = calls.call_bias_for_loops(loop_stats, thresholds=BiasThresholds(min_reads=min_pairs_loop, fdr=fdr))
+    loop_calls = calls.call_bias_for_loops(
+        loop_stats, thresholds=BiasThresholds(min_reads=min_pairs_loop, fdr=fdr)
+    )
 
     if validate_loops == "local":
         from .core.validate_local import run_local_validation
+
         loop_calls = run_local_validation(bam_handle, loops_df, loop_calls, anchor_pad, mapq)
 
     writers.write_peaks(out.with_suffix(".peaks.bed"), peak_calls)