samplesheet-parser 0.3.3__tar.gz → 0.3.4__tar.gz

{samplesheet_parser-0.3.3 → samplesheet_parser-0.3.4}/.gitignore

@@ -2,6 +2,8 @@
 BLOGPOST.md
 tests/fixtures/outputs/
 demo_output.txt
+**/CSBJ Submission/
+**/.claude/
 
 # Cache and build artifacts
 __pycache__/

{samplesheet_parser-0.3.3 → samplesheet_parser-0.3.4}/CHANGELOG.md

@@ -6,6 +6,53 @@ The format follows [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 ---
 
+## [0.3.4] - 2026-04-04
+
+### Added
+
+- **`samplesheet info` CLI command** — prints a concise summary of any V1 or
+  V2 sample sheet (format, sample count, lanes, index type, read lengths,
+  adapters, experiment name, instrument). Supports `--format json` for
+  machine-readable output; exits 0 on success, 2 on unreadable files.
+
+- **Configurable Hamming distance threshold** — `SampleSheetValidator.validate()`
+  now accepts a `min_hamming_distance` keyword argument (default: 3) so labs
+  using longer indexes can enforce stricter thresholds without changing the
+  module-level constant.
+  - `SampleSheetMerger` accepts the same parameter in `__init__()` and applies
+    it to both the intra-sheet and cross-sheet Hamming checks as well as the
+    post-merge validation step.
+  - `samplesheet validate` exposes `--min-hamming N` (must be ≥ 1; exits 2 on
+    invalid input). The JSON output includes `min_hamming_distance` for
+    auditability.
+
+- **`normalize_index_lengths()` utility** — normalizes index sequence lengths
+  across a list of sample dicts (output of `sheet.samples()`) to a consistent
+  length before merging sheets with mixed-length indexes.
+  - `strategy="trim"` — trims all indexes to the shortest sequence length.
+  - `strategy="pad"` — pads shorter indexes to the longest length using `"N"`
+    wildcard characters (supported by BCLConvert ≥ 3.9 and bcl2fastq ≥ 2.20).
+  - Auto-detects V1-style (`index`/`index2`) and V2-style (`Index`/`Index2`)
+    field names; explicit `index1_key`/`index2_key` overrides supported.
+  - Exported from the top-level package as `normalize_index_lengths`.
+
+- **CI / pre-commit integration guide** in README — GitHub Actions workflow
+  and pre-commit hook configuration for automatic sample sheet validation on
+  every commit or pull request that touches a `SampleSheet.csv`.
+
+### Fixed
+
+- `_detect_key()` in `index_utils` now selects the key with at least one
+  non-empty value before falling back to key presence, preventing silent
+  normalization skip when a key exists but all its values are `None` or `""`.
+
+### Changed
+
+- `--min-hamming` CLI option default and help text are now derived from the
+  `MIN_HAMMING_DISTANCE` constant in `validators.py` to prevent drift.
+
+---
+
 ## [0.3.3] - 2026-03-13
 
 ### Documentation

{samplesheet_parser-0.3.3 → samplesheet_parser-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: samplesheet-parser
-Version: 0.3.3
+Version: 0.3.4
 Summary: Format-agnostic parser for Illumina SampleSheet.csv files — supports IEM V1 and BCLConvert V2
 Project-URL: Homepage, https://github.com/chaitanyakasaraneni/samplesheet-parser
 Project-URL: Documentation, https://illumina-samplesheet.readthedocs.io
@@ -557,6 +557,80 @@ sheet.get_read_structure()   # → ReadStructure dataclass
 
 ---
 
+## CI / pre-commit integration
+
+The CLI exits with meaningful codes (`0` = clean, `1` = issues, `2` = error), making it easy to wire into automated pipelines.
+
+### GitHub Actions
+
+Add a validation step to any workflow that touches `SampleSheet.csv`:
+
+```yaml
+# .github/workflows/validate-samplesheet.yml
+name: Validate SampleSheet
+
+on:
+  push:
+    paths:
+      - '**/SampleSheet.csv'
+  pull_request:
+    paths:
+      - '**/SampleSheet.csv'
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - run: pip install "samplesheet-parser[cli]"
+
+      - name: Validate SampleSheet
+        run: samplesheet validate SampleSheet.csv --format json
+```
+
+### pre-commit hook
+
+Gate commits that touch any `SampleSheet.csv` in the repository:
+
+```yaml
+# .pre-commit-config.yaml
+repos:
+  - repo: local
+    hooks:
+      - id: samplesheet-validate
+        name: Validate SampleSheet.csv
+        entry: samplesheet validate
+        language: python
+        additional_dependencies: ["samplesheet-parser[cli]"]
+        files: SampleSheet\.csv$
+        pass_filenames: true
+```
+
+Install and run once to verify:
+
+```bash
+pip install pre-commit
+pre-commit install
+pre-commit run samplesheet-validate --all-files
+```
+
+### Stricter Hamming distance in CI
+
+If your lab uses longer indexes (10 bp+), raise the minimum Hamming distance threshold to catch borderline cases earlier:
+
+```bash
+samplesheet validate SampleSheet.csv --min-hamming 4
+```
+
+This is especially useful in CI where you want to prevent runs that will likely fail demultiplexing.
+
+---
+
 ## Contributing
 
 ```bash
@@ -585,7 +659,7 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for the full local testing guide and PR c
   title   = {samplesheet-parser: Format-agnostic parser for Illumina SampleSheet.csv},
   year    = {2026},
   url     = {https://github.com/chaitanyakasaraneni/samplesheet-parser},
-  version = {0.3.3}
+  version = {0.3.4}
 }
 ```
 

{samplesheet_parser-0.3.3 → samplesheet_parser-0.3.4}/README.md

@@ -506,6 +506,80 @@ sheet.get_read_structure()   # → ReadStructure dataclass
 
 ---
 
+## CI / pre-commit integration
+
+The CLI exits with meaningful codes (`0` = clean, `1` = issues, `2` = error), making it easy to wire into automated pipelines.
+
+### GitHub Actions
+
+Add a validation step to any workflow that touches `SampleSheet.csv`:
+
+```yaml
+# .github/workflows/validate-samplesheet.yml
+name: Validate SampleSheet
+
+on:
+  push:
+    paths:
+      - '**/SampleSheet.csv'
+  pull_request:
+    paths:
+      - '**/SampleSheet.csv'
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - run: pip install "samplesheet-parser[cli]"
+
+      - name: Validate SampleSheet
+        run: samplesheet validate SampleSheet.csv --format json
+```
+
+### pre-commit hook
+
+Gate commits that touch any `SampleSheet.csv` in the repository:
+
+```yaml
+# .pre-commit-config.yaml
+repos:
+  - repo: local
+    hooks:
+      - id: samplesheet-validate
+        name: Validate SampleSheet.csv
+        entry: samplesheet validate
+        language: python
+        additional_dependencies: ["samplesheet-parser[cli]"]
+        files: SampleSheet\.csv$
+        pass_filenames: true
+```
+
+Install and run once to verify:
+
+```bash
+pip install pre-commit
+pre-commit install
+pre-commit run samplesheet-validate --all-files
+```
+
+### Stricter Hamming distance in CI
+
+If your lab uses longer indexes (10 bp+), raise the minimum Hamming distance threshold to catch borderline cases earlier:
+
+```bash
+samplesheet validate SampleSheet.csv --min-hamming 4
+```
+
+This is especially useful in CI where you want to prevent runs that will likely fail demultiplexing.
+
+---
+
 ## Contributing
 
 ```bash
@@ -534,7 +608,7 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for the full local testing guide and PR c
   title   = {samplesheet-parser: Format-agnostic parser for Illumina SampleSheet.csv},
   year    = {2026},
   url     = {https://github.com/chaitanyakasaraneni/samplesheet-parser},
-  version = {0.3.3}
+  version = {0.3.4}
 }
 ```
 

{samplesheet_parser-0.3.3 → samplesheet_parser-0.3.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "samplesheet-parser"
-version = "0.3.3"
+version = "0.3.4"
 description = "Format-agnostic parser for Illumina SampleSheet.csv files — supports IEM V1 and BCLConvert V2"
 readme = "README.md"
 license = { file = "LICENSE" }

{samplesheet_parser-0.3.3 → samplesheet_parser-0.3.4}/samplesheet_parser/__init__.py

@@ -36,6 +36,7 @@ from samplesheet_parser.converter import SampleSheetConverter
 from samplesheet_parser.diff import DiffResult, SampleSheetDiff
 from samplesheet_parser.enums import IndexType, SampleSheetVersion
 from samplesheet_parser.factory import SampleSheetFactory
+from samplesheet_parser.index_utils import normalize_index_lengths
 from samplesheet_parser.merger import MergeResult, SampleSheetMerger
 from samplesheet_parser.parsers.v1 import SampleSheetV1
 from samplesheet_parser.parsers.v2 import SampleSheetV2
@@ -56,5 +57,6 @@ __all__ = [
     "SampleSheetWriter",
     "SampleSheetMerger",
     "MergeResult",
+    "normalize_index_lengths",
     "__version__",
 ]

{samplesheet_parser-0.3.3 → samplesheet_parser-0.3.4}/samplesheet_parser/cli.py

@@ -5,6 +5,7 @@ Entry point: ``samplesheet`` (configured in ``pyproject.toml``).
 
 Commands
 --------
+info        Show a quick summary of a sample sheet.
 validate    Validate a sheet — exit 0 if clean, exit 1 if errors.
 convert     Convert between V1 and V2 formats.
 diff        Diff two sheets — exit 1 if changes detected.
@@ -20,8 +21,12 @@ Usage
 -----
 ::
 
+    samplesheet info SampleSheet.csv
+    samplesheet info SampleSheet.csv --format json
+
     samplesheet validate SampleSheet.csv
     samplesheet validate SampleSheet.csv --format json
+    samplesheet validate SampleSheet.csv --min-hamming 4
 
     samplesheet convert SampleSheet_v1.csv --to v2 --output SampleSheet_v2.csv
     samplesheet convert SampleSheet_v2.csv --to v1 --output SampleSheet_v1.csv
@@ -50,6 +55,7 @@ except ImportError:  # pragma: no cover
     _TYPER_AVAILABLE = False
 
 from samplesheet_parser.enums import SampleSheetVersion
+from samplesheet_parser.validators import MIN_HAMMING_DISTANCE as _MIN_HAMMING_DEFAULT
 
 if _TYPER_AVAILABLE:
     app = typer.Typer(
@@ -115,6 +121,87 @@ if _TYPER_AVAILABLE:
             typer.echo(f"Error: unknown format '{fmt}'. Use 'text' or 'json'.", err=True)
             raise typer.Exit(code=2)
 
+    # ---------------------------------------------------------------------------
+    # info
+    # ---------------------------------------------------------------------------
+
+    @app.command()
+    def info(
+        path: Annotated[Path, typer.Argument(help="Path to SampleSheet.csv.", metavar="FILE")],
+        fmt: _FormatOption = "text",
+    ) -> None:
+        """Display a quick summary of a sample sheet without full validation.
+
+        Shows format version, sample count, lanes, index type, read lengths,
+        and adapter sequences at a glance.
+
+        Exits 0 on success, 2 on unreadable files.
+        """
+        from samplesheet_parser.factory import SampleSheetFactory
+        from samplesheet_parser.parsers.v1 import SampleSheetV1
+
+        _validate_fmt(fmt)
+        if not path.exists():
+            typer.echo(f"Error: file not found: {path}", err=True)
+            raise typer.Exit(code=2)
+
+        try:
+            factory = SampleSheetFactory()
+            sheet = factory.create_parser(str(path), parse=True, clean=False)
+        except Exception as exc:
+            typer.echo(f"Error: could not parse {path}: {exc}", err=True)
+            raise typer.Exit(code=2) from exc
+
+        if factory.version is None:  # pragma: no cover
+            raise RuntimeError("SampleSheetFactory.version must be set after create_parser")
+
+        samples = sheet.samples()
+        lanes = sorted({str(s.get("lane") or "") for s in samples} - {""}) or ["(none)"]
+        index_type = sheet.index_type()
+        adapters: list[str] = getattr(sheet, "adapters", []) or []
+        experiment_name: str | None = getattr(sheet, "experiment_name", None)
+
+        if isinstance(sheet, SampleSheetV1):
+            read_lengths = [str(r) for r in (sheet.read_lengths or [])]
+            instrument = sheet.instrument_type
+        else:
+            reads_dict = sheet.reads or {}
+            read_lengths = [
+                str(reads_dict[k])
+                for k in ("Read1Cycles", "Read2Cycles")
+                if k in reads_dict
+            ]
+            instrument = sheet.instrument_platform
+
+        if fmt == "json":
+            _print_json({
+                "file": str(path),
+                "format": factory.version.value,
+                "sample_count": len(samples),
+                "lanes": lanes,
+                "index_type": index_type,
+                "read_lengths": read_lengths,
+                "adapters": adapters,
+                "experiment_name": experiment_name,
+                "instrument": instrument,
+            })
+        else:
+            typer.echo(f"File:          {path}")
+            typer.echo(f"Format:        {factory.version.value}")
+            typer.echo(f"Samples:       {len(samples)}")
+            typer.echo(f"Lanes:         {', '.join(lanes)}")
+            typer.echo(f"Index type:    {index_type}")
+            typer.echo(
+                f"Read lengths:  {' + '.join(read_lengths) if read_lengths else '(not set)'}"
+            )
+            typer.echo(f"Adapters:      {', '.join(adapters) if adapters else '(none)'}")
+            if experiment_name:
+                typer.echo(f"Experiment:    {experiment_name}")
+            if instrument:
+                typer.echo(f"Instrument:    {instrument}")
+
+        raise typer.Exit(code=0)
+
     # ---------------------------------------------------------------------------
     # validate
     # ---------------------------------------------------------------------------
@@ -123,6 +210,17 @@ if _TYPER_AVAILABLE:
     def validate(
         path: Annotated[Path, typer.Argument(help="Path to SampleSheet.csv.", metavar="FILE")],
         fmt: _FormatOption = "text",
+        min_hamming: Annotated[
+            int,
+            typer.Option(
+                "--min-hamming",
+                help=(
+                    f"Minimum Hamming distance between indexes "
+                    f"(default: {_MIN_HAMMING_DEFAULT}, must be >= 1)."
+                ),
+                metavar="N",
+            ),
+        ] = _MIN_HAMMING_DEFAULT,
     ) -> None:
         """Validate a sample sheet for index, adapter, and structural issues.
 
@@ -134,6 +232,11 @@ if _TYPER_AVAILABLE:
         from samplesheet_parser.validators import SampleSheetValidator
 
         _validate_fmt(fmt)
+        if min_hamming < 1:
+            typer.echo(
+                f"Error: --min-hamming must be >= 1, got {min_hamming}.", err=True
+            )
+            raise typer.Exit(code=2)
         if not path.exists():
             typer.echo(f"Error: file not found: {path}", err=True)
             raise typer.Exit(code=2)
@@ -149,13 +252,14 @@ if _TYPER_AVAILABLE:
             raise RuntimeError("SampleSheetFactory.version must be set after create_parser")
         version = factory.version
 
-        result = SampleSheetValidator().validate(sheet)
+        result = SampleSheetValidator().validate(sheet, min_hamming_distance=min_hamming)
 
         if fmt == "json":
             _print_json({
                 "file": str(path),
                 "version": version.value,
                 "is_valid": result.is_valid,
+                "min_hamming_distance": min_hamming,
                 "errors": [
                     {"code": e.code, "message": e.message, "context": e.context}
                     for e in result.errors

samplesheet_parser-0.3.4/samplesheet_parser/index_utils.py

@@ -0,0 +1,184 @@
+"""
+Index normalization utilities for Illumina sample sheets.
+
+When merging sheets from different projects, indexes may have been designed
+with different lengths (e.g. 8 bp vs 10 bp).  This can cause
+``INDEX_DISTANCE_TOO_LOW`` or ``INDEX_COLLISION`` errors at merge time because
+the comparison is length-aware (shorter sequence wins).
+
+Two strategies are provided:
+
+``"trim"``
+    Trim all index sequences to the length of the *shortest* index in the
+    sample list.  Safe when the extra cycles are padding bases.
+
+``"pad"``
+    Pad shorter indexes to the length of the *longest* index using ``"N"``
+    wildcard characters.  ``"N"`` matches any base during demultiplexing in
+    BCLConvert ≥ 3.9 and bcl2fastq ≥ 2.20.
+
+Examples
+--------
+>>> from samplesheet_parser import SampleSheetFactory
+>>> from samplesheet_parser.index_utils import normalize_index_lengths
+>>>
+>>> sheet = SampleSheetFactory().create_parser("SampleSheet.csv", parse=True)
+>>> normalized = normalize_index_lengths(sheet.samples(), strategy="trim")
+>>> for s in normalized:
+...     print(s["sample_id"], s.get("index") or s.get("Index"))
+
+Authors
+-------
+Chaitanya Kasaraneni
+"""
+
+from __future__ import annotations
+
+from typing import Any, Literal
+
+
+def normalize_index_lengths(
+    samples: list[dict[str, Any]],
+    strategy: Literal["trim", "pad"] = "trim",
+    *,
+    index1_key: str | None = None,
+    index2_key: str | None = None,
+) -> list[dict[str, Any]]:
+    """Normalize index sequence lengths across all samples.
+
+    Detects whether the samples use V1-style keys (``"index"`` / ``"index2"``)
+    or V2-style keys (``"Index"`` / ``"Index2"``) automatically, unless
+    ``index1_key`` / ``index2_key`` are supplied explicitly.
+
+    Parameters
+    ----------
+    samples:
+        Output of ``sheet.samples()``.  Not modified in place — the
+        function returns new dicts with the index values replaced.
+    strategy:
+        ``"trim"`` — trim all indexes to the length of the shortest
+        sequence in *samples* (default).
+
+        ``"pad"``  — pad all indexes to the length of the longest
+        sequence using ``"N"`` wildcard characters.
+    index1_key:
+        Override the dict key for the primary index (I7).  Auto-detected
+        from the first sample that has an index value if ``None``.
+    index2_key:
+        Override the dict key for the secondary index (I5).  Auto-detected
+        from the first sample that has an index2 value if ``None``.  Pass
+        an explicit value of ``""`` to suppress I5 normalization entirely.
+
+    Returns
+    -------
+    list[dict]
+        Shallow copies of the input dicts with index values replaced.
+        Samples that have no index are returned unchanged.
+
+    Raises
+    ------
+    ValueError
+        If *strategy* is not ``"trim"`` or ``"pad"``.
+
+    Examples
+    --------
+    >>> samples = [
+    ...     {"sample_id": "S1", "index": "ATTACTCG",   "index2": "TATAGCCT"},
+    ...     {"sample_id": "S2", "index": "TCCGGAGAGG", "index2": "ATAGAGGCTA"},
+    ... ]
+    >>> normalize_index_lengths(samples, strategy="trim")
+    [{'sample_id': 'S1', 'index': 'ATTACTCG', 'index2': 'TATAGCCT'},
+     {'sample_id': 'S2', 'index': 'TCCGGAGA', 'index2': 'ATAGAGGC'}]
+
+    >>> normalize_index_lengths(samples, strategy="pad")
+    [{'sample_id': 'S1', 'index': 'ATTACTCGNN', 'index2': 'TATAGCCTNN'},
+     {'sample_id': 'S2', 'index': 'TCCGGAGAGG', 'index2': 'ATAGAGGCTA'}]
+    """
+    if strategy not in ("trim", "pad"):
+        raise ValueError(f"strategy must be 'trim' or 'pad', got {strategy!r}")
+
+    if not samples:
+        return []
+
+    # ── Auto-detect key names ────────────────────────────────────────────────
+    if index1_key is None:
+        index1_key = _detect_key(samples, ("index", "Index"))
+    if index2_key is None:
+        index2_key = _detect_key(samples, ("index2", "Index2"))
+
+    # ── Collect index lengths ────────────────────────────────────────────────
+    i1_lengths: list[int] = []
+    i2_lengths: list[int] = []
+
+    for s in samples:
+        if index1_key:
+            v = s.get(index1_key)
+            if v:
+                i1_lengths.append(len(v))
+        if index2_key:
+            v = s.get(index2_key)
+            if v:
+                i2_lengths.append(len(v))
+
+    # If all samples have the same length already, return copies unchanged.
+    i1_uniform = len(set(i1_lengths)) <= 1
+    i2_uniform = len(set(i2_lengths)) <= 1
+    if i1_uniform and i2_uniform:
+        return [dict(s) for s in samples]
+
+    # ── Determine target lengths ─────────────────────────────────────────────
+    if strategy == "trim":
+        target_i1 = min(i1_lengths) if i1_lengths else 0
+        target_i2 = min(i2_lengths) if i2_lengths else 0
+    else:  # pad
+        target_i1 = max(i1_lengths) if i1_lengths else 0
+        target_i2 = max(i2_lengths) if i2_lengths else 0
+
+    # ── Apply normalization ──────────────────────────────────────────────────
+    result: list[dict[str, Any]] = []
+    for sample in samples:
+        out = dict(sample)
+
+        if index1_key and target_i1:
+            v1: str | None = out.get(index1_key)  # type: ignore[assignment]
+            if v1:
+                out[index1_key] = _apply(v1, target_i1, strategy)
+
+        if index2_key and target_i2:
+            v2: str | None = out.get(index2_key)  # type: ignore[assignment]
+            if v2:
+                out[index2_key] = _apply(v2, target_i2, strategy)
+
+        result.append(out)
+
+    return result
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+def _detect_key(samples: list[dict[str, Any]], candidates: tuple[str, ...]) -> str:
+    """Return the first candidate key that has at least one non-empty value.
+
+    Falls back to key *presence* (regardless of value) if no candidate has
+    any non-empty value, and finally to the first candidate name if none are
+    present at all.
+    """
+    # Prefer a key that actually carries data
+    for key in candidates:
+        if any(s.get(key) for s in samples):
+            return key
+    # Fall back to key presence (all values empty/None but key exists)
+    for key in candidates:
+        if any(key in s for s in samples):
+            return key
+    return candidates[0]
+
+
+def _apply(seq: str, target_length: int, strategy: str) -> str:
+    """Trim or pad *seq* to *target_length*."""
+    if strategy == "trim":
+        return seq[:target_length]
+    # pad
+    return seq.ljust(target_length, "N")

{samplesheet_parser-0.3.3 → samplesheet_parser-0.3.4}/samplesheet_parser/merger.py

@@ -167,6 +167,11 @@ class SampleSheetMerger:
         Output format for the merged sheet. Defaults to
         :attr:`SampleSheetVersion.V2`. If inputs are mixed V1/V2, all
         are converted to this format.
+    min_hamming_distance:
+        Minimum Hamming distance required between any two index sequences
+        in the same lane, both within a sheet and across sheets. Pairs
+        below this threshold produce an ``INDEX_DISTANCE_TOO_LOW`` warning.
+        Defaults to :data:`MIN_HAMMING_DISTANCE` (3).
 
     Examples
     --------
@@ -181,8 +186,11 @@ class SampleSheetMerger:
     def __init__(
         self,
         target_version: SampleSheetVersion = SampleSheetVersion.V2,
+        *,
+        min_hamming_distance: int = MIN_HAMMING_DISTANCE,
     ) -> None:
         self.target_version = target_version
+        self.min_hamming_distance = min_hamming_distance
         self._paths: list[Path] = []
 
     # ------------------------------------------------------------------
@@ -267,7 +275,7 @@ class SampleSheetMerger:
         self._check_read_lengths(parsed, result)
         self._check_adapters(parsed, result)
         self._check_index_collisions(parsed, result)
-        self._check_index_distances(parsed, result)
+        self._check_index_distances(parsed, result, min_distance=self.min_hamming_distance)
 
         # ── 3. Abort early if hard conflicts found ───────────────────────
         if result.has_conflicts and abort_on_conflicts:
@@ -688,7 +696,9 @@ class SampleSheetMerger:
             sheet = SampleSheetFactory().create_parser(
                 tmp_path, parse=True, clean=False
             )
-            vresult = SampleSheetValidator().validate(sheet)
+            vresult = SampleSheetValidator().validate(
+                sheet, min_hamming_distance=self.min_hamming_distance
+            )
         except Exception as exc:
             # Convert any parse/validation failure into a structured conflict
             # so merge() always returns a MergeResult rather than raising.