countmut 0.1.2__tar.gz → 0.1.4__tar.gz

{countmut-0.1.2 → countmut-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: countmut
-Version: 0.1.2
+Version: 0.1.4
 Summary: Unified ultra-fast strand-aware mutation counter (C backend + samtools-style -e/-p filters)
 Author-email: Ye Chang <yech1990@gmail.com>
 License-Expression: MIT

{countmut-0.1.2 → countmut-0.1.4}/countmut/backend.py

@@ -100,7 +100,7 @@ def _build_cmd(
         "--threads",
         str(ecfg.threads or min(os.cpu_count() or 1, 8)),
         "--max-depth",
-        str(fcfg.max_depth or 8000),
+        str(fcfg.max_depth),   # 0 = unlimited
     ]
     if fcfg.max_unc is not None:
         cmd += ["--max-unc", str(fcfg.max_unc)]
@@ -137,12 +137,24 @@ def _build_cmd(
             cmd.append("--vcf")
     if ecfg.min_depth:
         cmd += ["--min-depth", str(ecfg.min_depth)]
+    if ecfg.verbose:
+        cmd.append("--verbose")
     return cmd
 
 
 # ---------------------------------------------------------------------------
 # public entry point
 # ---------------------------------------------------------------------------
+def _forward_stderr(stream) -> None:
+    """Forward a child process' stderr lines to our stderr (--verbose)."""
+    try:
+        for line in stream:
+            sys.stderr.write(line)
+            sys.stderr.flush()
+    except (ValueError, OSError):
+        pass
+
+
 def run_backend(
     samfile: str,
     reference: str,
@@ -190,12 +202,27 @@ def run_backend(
         ecfg=ecfg,
     )
     start = time.time()
-    proc = subprocess.run(cmd, capture_output=True, text=True)
+    stdout = ""
+    if ecfg.verbose:
+        # stream the C core's stderr (progress) to our stderr in real time
+        proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
+        import threading
+
+        fwd = threading.Thread(
+            target=_forward_stderr, args=(proc.stderr,), daemon=True
+        )
+        fwd.start()
+        out, _ = proc.communicate()
+        fwd.join(timeout=2)
+        stdout = out or ""
+    else:
+        proc = subprocess.run(cmd, capture_output=True, text=True)
+        stdout = proc.stdout
     elapsed = time.time() - start
 
     if output is None and proc.returncode == 0:
-        # stream the TSV from stdout (already printed by the binary)
-        sys.stdout.write(proc.stdout)
+        # stream the TSV from stdout
+        sys.stdout.write(stdout)
         sys.stdout.flush()
 
     rows = 0
@@ -203,7 +230,7 @@ def run_backend(
         with open(output) as fh:
             rows = sum(1 for _ in fh) - 1
     else:
-        rows = len(proc.stdout.splitlines()) - 1
+        rows = len(stdout.splitlines()) - 1
 
     if proc.returncode != 0:
         sys.stderr.write(f"[countmut] backend error: {proc.stderr}\n")

{countmut-0.1.2 → countmut-0.1.4}/countmut/cli.py

@@ -26,7 +26,7 @@ from .model import EngineConfig, FilterConfig, MutationConfig, StrandConfig
 try:
     __version__ = importlib_metadata.version("countmut")
 except importlib_metadata.PackageNotFoundError:  # pragma: no cover
-    __version__ = "0.1.2"
+    __version__ = "0.1.4"
 
 click.rich_click.TEXT_MARKUP = "rich"
 click.rich_click.SHOW_ARGUMENTS = True
@@ -144,6 +144,13 @@ console = Console()
     show_default=True,
     help="Minimum site depth to report (base/allele mode)",
 )
+@click.option(
+    "--max-depth",
+    type=int,
+    default=0,
+    show_default=True,
+    help="Per-position depth cap (pileup engine; 0 = unlimited, counts all reads)",
+)
 @click.option(
     "--min-allele-support",
     type=int,
@@ -166,7 +173,12 @@ console = Console()
     default=None,
     help="Lua site filter (e.g. \"ref == 'A' and depth >= 5 and g > 2\")",
 )
-@click.option("--verbose", is_flag=True, default=False, help="Verbose logging")
+@click.option(
+    "--verbose",
+    is_flag=True,
+    default=False,
+    help="Real-time per-region progress on stderr (large BAMs)",
+)
 def main(
     samfile,
     reference,
@@ -182,6 +194,7 @@ def main(
     split_strand,
     count_indels,
     min_depth,
+    max_depth,
     min_allele_support,
     vcf,
     read_expr,
@@ -202,6 +215,7 @@ def main(
         min_con=1,
         trim_start=2,
         trim_end=2,
+        max_depth=max_depth,
     )
     mcfg = (
         MutationConfig(
@@ -223,6 +237,7 @@ def main(
         vcf=vcf,
         read_expr=read_expr,
         pile_expr=pile_expr,
+        verbose=verbose,
     )
 
     config_table = Table(box=rich.box.MINIMAL, show_header=False)

{countmut-0.1.2 → countmut-0.1.4}/countmut/model.py

@@ -85,5 +85,6 @@ class EngineConfig:
     vcf: bool = False  # allele mode: emit VCF
     count_indels: bool = False
     split_strand: bool = True
+    verbose: bool = False  # real-time per-region progress on stderr
     report_reference_bases: bool = False  # -k flanking window (pbr)
     flanking: int = 0

{countmut-0.1.2 → countmut-0.1.4}/countmut.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: countmut
-Version: 0.1.2
+Version: 0.1.4
 Summary: Unified ultra-fast strand-aware mutation counter (C backend + samtools-style -e/-p filters)
 Author-email: Ye Chang <yech1990@gmail.com>
 License-Expression: MIT

{countmut-0.1.2 → countmut-0.1.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "countmut"
-version = "0.1.2"
+version = "0.1.4"
 description = "Unified ultra-fast strand-aware mutation counter (C backend + samtools-style -e/-p filters)"
 readme = "README.md"
 license = "MIT"