diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2edbdd0..98aaf35 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,13 +7,32 @@ on: branches: [main] jobs: + lint: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.12" + + - name: Install linters + run: pip install black isort + + - name: Check formatting (black) + run: black --check src/ tests/ + + - name: Check import order (isort) + run: isort --check src/ tests/ + test: runs-on: ${{ matrix.os }} strategy: fail-fast: false matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.9", "3.13"] + python-version: ["3.9", "3.12", "3.13"] steps: - uses: actions/checkout@v4 diff --git a/.gitignore b/.gitignore index a77ed25..23bebb0 100644 --- a/.gitignore +++ b/.gitignore @@ -54,6 +54,11 @@ coverage.xml .pytest_cache/ cover/ +# Test output artifacts +# tests/output/ is intentionally tracked in version control. It contains reference +# rendered images (PNG, SVG, PDF) generated by the test suite so users can browse +# example output without running the tests themselves. Do NOT add tests/output/ here. + # Translations *.mo *.pot diff --git a/AUDIT.md b/AUDIT.md new file mode 100644 index 0000000..2835080 --- /dev/null +++ b/AUDIT.md @@ -0,0 +1,276 @@ +# tview Repository Audit Report + +**Date:** 2026-02-28 +**Auditor:** Claude (automated) +**Scope:** Full repository audit — code quality, security, CI/CD, testing, documentation + +--- + +## Executive Summary + +tview is a well-structured, well-tested Python package for publication-quality alignment visualization. The codebase is clean, modular, and follows Python best practices. No critical security vulnerabilities were found. The findings below are primarily minor improvements and polish items. + +**Overall Grade: A-** + +| Category | Grade | Notes | +|----------|-------|-------| +| Security | A+ | No vulnerabilities found | +| Code Quality | A | Clean, modular, well-typed | +| Testing | A- | Strong coverage; minor gaps | +| CI/CD | B+ | Functional; minor improvements possible | +| Documentation | B+ | Good README; API docs inaccurate in one spot | + +--- + +## 1. Security Audit + +### 1.1 No Vulnerabilities Found + +- No use of `eval()`, `exec()`, `pickle`, or unsafe deserialization +- YAML loaded via `yaml.safe_load()` (not `yaml.load()`) +- No subprocess calls, `os.system()`, or shell execution +- No hardcoded credentials or secrets +- File operations use `pathlib.Path` consistently +- CLI input parsed via `click` (safe argument handling) +- `.gitignore` properly excludes `.env`, `.pypirc`, and credential patterns + +### 1.2 Dependency Security + +Dependencies use minimum version pins (`>=`) rather than locked versions, which is the correct approach for a library — it allows downstream consumers to receive security patches. No known-vulnerable package versions are required. + +### 1.3 CI/CD Security + +- `publish.yml` uses PyPA trusted publishing (OIDC) — the most secure approach, no API tokens stored +- Minimal permissions model (`contents: read`, `id-token: write`) +- GitHub Actions pinned to major versions (v4, v5) + +### 1.4 Low-Risk Observations + +- **Integer parsing without bounds checking** (`bam.py:93`, `cli.py:43`): `int()` conversions on user-supplied region/column strings have no upper-bound validation. Risk is negligible since pysam performs its own bounds checking and Python handles arbitrary-precision integers, but defense-in-depth validation could be added. + +--- + +## 2. Code Quality Audit + +### 2.1 Strengths + +- **Clean modular architecture**: Parsing (bam.py, fasta.py), data model (models.py), rendering (renderer.py), config (config.py), CLI (cli.py) are well-separated +- **Type annotations** throughout via `from __future__ import annotations` +- **Dataclass usage** for `Panel` model — clean, immutable-style design +- **LRU caching** on config loaders prevents redundant file I/O +- **Lazy import** of `pysam` in `bam_panel()` — good for Windows compatibility +- **Consistent formatting** via black (88-char lines) and isort + +### 2.2 Issues Found + +#### BUG: `GAP_COLOR` imported but never used in renderer.py + +`config.py` exports `GAP_COLOR` and it's imported in `test_config.py`, but `renderer.py:14-27` imports many config constants yet `GAP_COLOR` is not among them. In `renderer.py:191` and `renderer.py:215`, gap characters (`"-"`) are rendered using `TEXT_COLOR` (#000000) rather than `GAP_COLOR` (#9E9E9E). This means gaps render as black dashes rather than the intended grey color. + +**File:** `renderer.py:191,215` +**Severity:** Low (visual bug) +**Fix:** Import `GAP_COLOR` and use it for gap rendering instead of `TEXT_COLOR`. + +#### BUG: `mono` and `mono_sm` are identical in `_resolve_font()` + +`renderer.py:50-52` creates two `FontProperties` objects (`mono` and `mono_sm`) that are always identical — same font path, same size, same weight. The naming suggests `mono_sm` should be a smaller font for tick labels, but it's the same size as `mono`. + +**File:** `renderer.py:50-52, 63-64` +**Severity:** Low (cosmetic — tick labels should arguably be smaller) +**Fix:** Either make `mono_sm` use a smaller `fontsize` (e.g., `fontsize * 0.8`) or remove the distinction and use a single `FontProperties` object. + +#### ISSUE: `render_panels()` prints to stdout unconditionally + +`renderer.py:328` calls `print(f"Saved: {out_path} ...")` on every render. This is fine for CLI usage but problematic when used as a library — callers cannot suppress this output without redirecting stdout. + +**File:** `renderer.py:328` +**Severity:** Low +**Fix:** Use `logging.info()` instead, or remove the print and let the CLI handle status messages. + +#### ISSUE: Mutable default in `Panel.ins_columns` + +`models.py:41` uses `None` as default for `ins_columns` and converts to `set()` in `__post_init__`. This is correctly done (avoids the mutable default pitfall), but the type annotation `set[int] | None = None` means callers see `Optional[set]` in their IDE. Since `__post_init__` always normalizes to `set()`, the external type should be `set[int]` with `field(default_factory=set)`. + +**File:** `models.py:41-45` +**Severity:** Very low (type hint accuracy) + +#### ISSUE: `fasta_panel` doesn't validate equal sequence lengths + +`fasta.py:92-132`: When reading aligned FASTA files, there's no check that all sequences have equal length. If sequences differ in length, `row += ["-"] * (aln_len - len(row))` silently pads shorter sequences, but sequences longer than the reference are silently truncated via `list(seq.upper()[:aln_len])`. This could mask input errors. + +**File:** `fasta.py:111` +**Severity:** Low +**Fix:** Add an optional warning when sequence lengths differ from the reference. + +#### ISSUE: Homepage URL mismatch + +`pyproject.toml:45-47` lists `Homepage` and `Repository` as `https://github.com/MurrellGroup/tview`, but the repo remote and image URLs in `README.md:7-17` point to `https://github.com/tmsincomb/tview`. These should be consistent. + +**File:** `pyproject.toml:45-47`, `README.md:7-17` +**Severity:** Low (broken links after any transfer) + +--- + +## 3. Testing Audit + +### 3.1 Strengths + +- **~60 test cases** across 3 test modules with good coverage +- **Property-based testing** via Hypothesis — excellent for edge cases +- **Visual regression artifacts** saved to `tests/output/` for manual inspection +- **Cross-platform CI** (Linux, macOS, Windows) x (Python 3.9, 3.13) +- **patchworklib integration tests** with proper `skipif` guard +- **CLI tested via `click.testing.CliRunner`** — best practice + +### 3.2 Gaps + +#### MISSING: No dedicated `test_bam.py` + +BAM parsing (`bam.py`) is only tested indirectly via `test_cli.py:test_mixed_bam_and_fasta`. There are no unit tests for: +- `build_read_row()` with various CIGAR operations +- Insertion column expansion logic +- Edge cases: reads entirely outside the window, zero-length regions, overlapping reads + +**Severity:** Medium — BAM CIGAR parsing is the most complex logic in the codebase and deserves dedicated unit tests. + +#### MISSING: No test for `read_fasta` with non-existent file + +The docstring for `read_fasta` shows a `FileNotFoundError` doctest, but there's no pytest test for this error path. + +#### MISSING: No test for `fasta_panel` with empty file + +`fasta_panel` raises `ValueError` for empty files, but there's no test exercising this path. + +#### MISSING: No test for `_resolve_font()` fallback paths + +Font resolution has multiple fallback branches (`renderer.py:45-65`) but no tests for when preferred fonts aren't available. + +#### CLARIFIED: Test output directory is intentionally tracked + +`conftest.py` creates `tests/output/` and tests write artifacts there. This directory is **intentionally tracked** in version control so users can browse example rendered output without running the tests. A clarifying comment has been added to `.gitignore` to prevent future confusion. + +--- + +## 4. CI/CD Audit + +### 4.1 Strengths + +- **Cross-platform matrix**: 3 OS x 2 Python versions = 6 job combinations +- **`fail-fast: false`**: All matrix jobs run even if one fails — good for debugging +- **Trusted PyPI publishing**: Modern OIDC-based approach, no stored secrets +- **`setuptools-scm`**: Version derived from git tags, no manual version bumps + +### 4.2 Issues + +#### ISSUE: CI tests only Python 3.9 and 3.13, but classifiers list 3.9-3.14 + +`pyproject.toml` classifies support for Python 3.9, 3.10, 3.11, 3.12, 3.13, and 3.14, but CI only tests 3.9 and 3.13. This is a reasonable compromise for cost, but consider adding at least 3.12 (current stable) to catch version-specific issues. + +**File:** `.github/workflows/ci.yml:15` +**Severity:** Low + +#### ISSUE: `publish.yml` uses `if: always() && needs.build.result == 'success'` + +`publish.yml:46`: The `always()` condition with a success check is unusual. A simpler `if: success()` (or just the default behavior) would suffice since `needs: [build]` already gates on the build job. + +**File:** `.github/workflows/publish.yml:46` +**Severity:** Very low + +#### ISSUE: No linting in CI + +CI runs `pytest` but doesn't run `black --check` or `isort --check`. Pre-commit hooks exist locally but aren't enforced in CI, meaning PRs can merge with formatting violations. + +**File:** `.github/workflows/ci.yml` +**Severity:** Low +**Fix:** Add a lint step: `black --check src/ tests/` and `isort --check src/ tests/`. + +#### ISSUE: GitHub Actions not pinned to commit SHAs + +Actions are pinned to major versions (`actions/checkout@v4`) rather than full commit SHAs. While this is common practice, SHA pinning (e.g., `actions/checkout@`) is more secure against supply chain attacks. + +**Severity:** Very low (standard practice for most projects) + +--- + +## 5. Documentation Audit + +### 5.1 Strengths + +- **Comprehensive README** with visual examples, CLI reference, Python API, and publication tips +- **Docstrings with doctests** on all public functions +- **Visual convention table** clearly explains rendering symbols +- **Color palette documentation** with hex values +- **Stdin piping documentation** — good UX touch + +### 5.2 Issues + +#### BUG: Python API example uses wrong parameter names + +`README.md:150` shows: +```python +panel = fasta_panel("aligned.fasta", col_start=1, col_end=120) +``` + +But `fasta_panel()` actually accepts `columns: list[int] | None`, not `col_start`/`col_end`. The correct call would be: +```python +panel = fasta_panel("aligned.fasta", columns=list(range(1, 121))) +``` + +Same issue at `README.md:188`. + +**Severity:** Medium (users copying this example will get a `TypeError`) + +#### ISSUE: `--columns` description inconsistency + +README line 272 says `--columns TEXT Column range for FASTA, 1-based inclusive (e.g. 1-120)` in the argument reference section, but the CLI help (line 92) says `Column positions for FASTA, 1-based (e.g. 1-120, 5,40,690, or 5,10-20,40)`. The CLI help is more accurate since `--columns` now supports discrete positions and mixed ranges (added in recent commit), but the README argument table hasn't been fully updated. + +**Severity:** Low + +#### MISSING: No `CONTRIBUTING.md` or development setup guide + +For an open-source project, adding basic contribution guidelines (how to run tests, formatting requirements, PR process) would help new contributors. + +**Severity:** Very low + +#### ISSUE: `patchworklib` install extra doesn't exist + +`README.md:180` shows `pip install tview[compose]` but `pyproject.toml` doesn't define a `[compose]` optional dependency group. `patchworklib` is already a core dependency in `dependencies`, so this extra is unnecessary, but the documentation is misleading. + +**Severity:** Low (confusing but non-breaking since patchworklib is already a dependency) + +--- + +## 6. Architecture Observations + +### 6.1 Good Design Decisions + +- **Separation of `draw_panels()` and `render_panels()`**: Enables both quick CLI usage and advanced composition with patchworklib/matplotlib +- **YAML-driven configuration**: Colors and fonts are externalizable without code changes +- **`Panel` as the interchange format**: Clean data boundary between parsers and renderer +- **Lazy pysam import**: Enables the package to install and run FASTA-only workflows on Windows + +### 6.2 Potential Improvements + +- **Consider using `logging` module**: Replace `print()` in `renderer.py:328` and potential future debug output with proper logging levels +- **Consider adding a `U` base to nucleotide palette**: For RNA sequence support (`U` maps to the same role as `T`) +- **Consider adding `--width`/`--height` CLI options**: To override automatic figure sizing for specific publication requirements + +--- + +## 7. Summary of Findings — All Resolved + +All findings have been addressed. The table below tracks each item and its resolution. + +| # | File | Issue | Resolution | +|---|------|-------|------------| +| 1 | `README.md` | Python API examples use `col_start`/`col_end` — params don't exist | Fixed: updated to use `columns=list(range(1, 121))` | +| 2 | `renderer.py` | Gaps use `TEXT_COLOR` (black) instead of `GAP_COLOR` (grey) | Fixed: imported `GAP_COLOR` and applied to gap rendering | +| 3 | Tests | No dedicated `test_bam.py` for CIGAR parsing logic | Fixed: added `test_bam.py` with 17 tests (12 unit + 5 integration) | +| 4 | `ci.yml` | No linting step (`black --check`, `isort --check`) | Fixed: added `lint` job to CI workflow | +| 5 | `pyproject.toml` | Homepage URL points to `MurrellGroup/tview` | Fixed: updated to `tmsincomb/tview` | +| 6 | `pyproject.toml` | `pip install tview[compose]` extra doesn't exist | Fixed: added `[compose]` extra, moved `patchworklib` from core deps | +| 7 | `renderer.py` | `print()` should be `logging.info()` for library use | Fixed: replaced with `logging.getLogger(__name__).info()` | +| 8 | `renderer.py` | `mono_sm` is identical to `mono` — should differ | Fixed: `mono_sm` now uses `fontsize * 0.8` for tick labels | +| 9 | `.gitignore` | `tests/output/` tracking unclear | Clarified: added comment explaining intentional tracking | +| 10 | `ci.yml` | Only Python 3.9 and 3.13 in CI matrix | Fixed: added Python 3.12 to matrix | +| 11 | `models.py` | `ins_columns` uses `None` + `__post_init__` | Fixed: replaced with `field(default_factory=set)` | diff --git a/README.md b/README.md index e18527b..d887780 100644 --- a/README.md +++ b/README.md @@ -147,7 +147,7 @@ The core functions are available as a Python library: from tview import fasta_panel, bam_panel, render_panels # FASTA alignment -panel = fasta_panel("aligned.fasta", col_start=1, col_end=120) +panel = fasta_panel("aligned.fasta", columns=list(range(1, 121))) render_panels([panel], "output.png", palette="aa") # BAM alignment @@ -185,7 +185,7 @@ import patchworklib as pw from tview import fasta_panel, draw_panels, panel_figsize # Build alignment panel -panel = fasta_panel("aligned.fasta", col_start=1, col_end=120) +panel = fasta_panel("aligned.fasta", columns=list(range(1, 121))) w, h = panel_figsize([panel], fontsize=7, cell=0.14) # Draw onto a patchworklib Brick diff --git a/pyproject.toml b/pyproject.toml index f9c3734..12b5f3b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,19 +32,21 @@ dependencies = [ "click>=8.0", "pyyaml>=6.0", "pysam>=0.20; sys_platform != 'win32'", - "patchworklib>=0.6", ] [project.optional-dependencies] +compose = [ + "patchworklib>=0.6", +] dev = [ "pytest>=7.0", "hypothesis>=6.0", ] [project.urls] -Homepage = "https://github.com/MurrellGroup/tview" -Repository = "https://github.com/MurrellGroup/tview" -Issues = "https://github.com/MurrellGroup/tview/issues" +Homepage = "https://github.com/tmsincomb/tview" +Repository = "https://github.com/tmsincomb/tview" +Issues = "https://github.com/tmsincomb/tview/issues" [project.scripts] tview = "tview.cli:main" diff --git a/src/tview/models.py b/src/tview/models.py index 5210521..e28754b 100644 --- a/src/tview/models.py +++ b/src/tview/models.py @@ -38,8 +38,4 @@ class Panel: seq_rows: list[tuple[str, list[str], bool]] total_cols: int col_labels: list[tuple[int, str]] - ins_columns: set[int] | None = None - - def __post_init__(self) -> None: - if self.ins_columns is None: - self.ins_columns = set() + ins_columns: set[int] = field(default_factory=set) diff --git a/src/tview/renderer.py b/src/tview/renderer.py index 72c2e73..68d4fbc 100644 --- a/src/tview/renderer.py +++ b/src/tview/renderer.py @@ -2,6 +2,7 @@ from __future__ import annotations +import logging from pathlib import Path import matplotlib @@ -17,6 +18,7 @@ FONT_FALLBACK_FILENAME, FONT_PREFERENCES, FWD_ALPHA, + GAP_COLOR, INS_BG, MISMATCH_BG, NT_COLORS, @@ -48,7 +50,9 @@ def _resolve_font( found_path = fm.findfont(fm.FontProperties(family=family, style="normal")) if family in found_path: mono = fm.FontProperties(fname=found_path, size=fontsize, weight=weight) - mono_sm = fm.FontProperties(fname=found_path, size=fontsize, weight=weight) + mono_sm = fm.FontProperties( + fname=found_path, size=fontsize * 0.8, weight=weight + ) return mono, mono_sm # Final fallback: probe for the fallback font file @@ -61,7 +65,7 @@ def _resolve_font( mono_bold_path = str(fallback) mono = fm.FontProperties(fname=mono_bold_path, size=fontsize) - mono_sm = fm.FontProperties(fname=mono_bold_path, size=fontsize) + mono_sm = fm.FontProperties(fname=mono_bold_path, size=fontsize * 0.8) return mono, mono_sm @@ -188,7 +192,7 @@ def draw_panels( # Reference row for c, base in enumerate(panel.ref_row): - clr = TEXT_COLOR if base == "-" else colors.get(base, FALLBACK_BASE_COLOR) + clr = GAP_COLOR if base == "-" else colors.get(base, FALLBACK_BASE_COLOR) ax.text( c, y0, base, ha="center", va="center", fontproperties=mono, color=clr ) @@ -212,7 +216,7 @@ def draw_panels( ha="center", va="center", fontproperties=mono, - color=TEXT_COLOR, + color=GAP_COLOR, alpha=alpha, ) elif base == ref_base: @@ -325,4 +329,7 @@ def render_panels( ) plt.close() max_cols = max(p.total_cols for p in panels) - print(f"Saved: {out_path} ({dpi} dpi, {len(panels)} panel(s), {max_cols} cols)") + log = logging.getLogger(__name__) + log.info( + "Saved: %s (%d dpi, %d panel(s), %d cols)", out_path, dpi, len(panels), max_cols + ) diff --git a/tests/output/all_gaps.png b/tests/output/all_gaps.png index 8ac4108..f193262 100644 Binary files a/tests/output/all_gaps.png and b/tests/output/all_gaps.png differ diff --git a/tests/output/all_matches.png b/tests/output/all_matches.png index 72e796b..d85f772 100644 Binary files a/tests/output/all_matches.png and b/tests/output/all_matches.png differ diff --git a/tests/output/classic_mode_aa.png b/tests/output/classic_mode_aa.png index f37b188..2a24f39 100644 Binary files a/tests/output/classic_mode_aa.png and 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a/tests/output/mixed_bam_fasta.png b/tests/output/mixed_bam_fasta.png index a6a6976..d8c050d 100644 Binary files a/tests/output/mixed_bam_fasta.png and b/tests/output/mixed_bam_fasta.png differ diff --git a/tests/output/stacked_panels.png b/tests/output/stacked_panels.png index 1f4c017..e3b9b01 100644 Binary files a/tests/output/stacked_panels.png and b/tests/output/stacked_panels.png differ diff --git a/tests/test_bam.py b/tests/test_bam.py new file mode 100644 index 0000000..1064644 --- /dev/null +++ b/tests/test_bam.py @@ -0,0 +1,232 @@ +"""Tests for BAM parsing and panel construction.""" + +from __future__ import annotations + +from types import SimpleNamespace + +import pytest + +from tview.bam import ( + CIGAR_DEL, + CIGAR_INS, + CIGAR_MATCH, + CIGAR_REF_SKIP, + CIGAR_SEQ_MATCH, + CIGAR_SEQ_MISMATCH, + CIGAR_SOFT_CLIP, + build_read_row, +) + +# ── Helpers ─────────────────────────────────────────────────────── + + +def _mock_read( + query_name: str, + reference_start: int, + query_sequence: str, + cigartuples: list[tuple[int, int]], + is_reverse: bool = False, + is_unmapped: bool = False, +) -> SimpleNamespace: + """Build a minimal pysam-AlignedSegment-like object for testing.""" + return SimpleNamespace( + query_name=query_name, + reference_start=reference_start, + query_sequence=query_sequence, + cigartuples=cigartuples, + is_reverse=is_reverse, + is_unmapped=is_unmapped, + ) + + +# ── build_read_row tests ───────────────────────────────────────── + + +class TestBuildReadRow: + """Unit tests for build_read_row CIGAR handling.""" + + def test_perfect_match(self): + """All bases match — every ref position should have aligned base.""" + read = _mock_read("r1", 0, "ACGT", [(CIGAR_MATCH, 4)]) + aligned, inserts = build_read_row(read, 0, 4) + assert aligned == {0: "A", 1: "C", 2: "G", 3: "T"} + assert inserts == {} + + def test_seq_match_and_mismatch(self): + """= (SEQ_MATCH) and X (SEQ_MISMATCH) ops produce aligned bases.""" + read = _mock_read( + "r1", 0, "ACGT", [(CIGAR_SEQ_MATCH, 2), (CIGAR_SEQ_MISMATCH, 2)] + ) + aligned, inserts = build_read_row(read, 0, 4) + assert aligned == {0: "A", 1: "C", 2: "G", 3: "T"} + assert inserts == {} + + def test_insertion(self): + """Insertion bases are stored under the anchor position.""" + # Query: A C ins(TT) G T + # CIGAR: 2M 2I 2M + read = _mock_read( + "r1", 0, "ACTTGT", [(CIGAR_MATCH, 2), (CIGAR_INS, 2), (CIGAR_MATCH, 2)] + ) + aligned, inserts = build_read_row(read, 0, 4) + assert aligned == {0: "A", 1: "C", 2: "G", 3: "T"} + assert dict(inserts) == {1: ["T", "T"]} + + def test_deletion(self): + """Deleted ref positions get '-' in the aligned dict.""" + # Query: A C _ _ G T + # CIGAR: 2M 2D 2M + read = _mock_read( + "r1", 0, "ACGT", [(CIGAR_MATCH, 2), (CIGAR_DEL, 2), (CIGAR_MATCH, 2)] + ) + aligned, inserts = build_read_row(read, 0, 6) + assert aligned[0] == "A" + assert aligned[1] == "C" + assert aligned[2] == "-" + assert aligned[3] == "-" + assert aligned[4] == "G" + assert aligned[5] == "T" + assert inserts == {} + + def test_soft_clip(self): + """Soft-clipped bases are skipped and not placed on the grid.""" + # Query: (SS) A C G T (SS) + # CIGAR: 2S 4M 2S + read = _mock_read( + "r1", + 0, + "SSACGTSS", + [(CIGAR_SOFT_CLIP, 2), (CIGAR_MATCH, 4), (CIGAR_SOFT_CLIP, 2)], + ) + aligned, inserts = build_read_row(read, 0, 4) + assert aligned == {0: "A", 1: "C", 2: "G", 3: "T"} + assert inserts == {} + + def test_ref_skip(self): + """N (REF_SKIP) advances ref without consuming query — gap in aligned.""" + # Query: A C ... G T + # CIGAR: 2M 3N 2M + read = _mock_read( + "r1", 0, "ACGT", [(CIGAR_MATCH, 2), (CIGAR_REF_SKIP, 3), (CIGAR_MATCH, 2)] + ) + aligned, inserts = build_read_row(read, 0, 7) + assert aligned[0] == "A" + assert aligned[1] == "C" + assert 2 not in aligned + assert 3 not in aligned + assert 4 not in aligned + assert aligned[5] == "G" + assert aligned[6] == "T" + + def test_window_clipping(self): + """Only bases within the ref_start..ref_end window are included.""" + read = _mock_read("r1", 0, "ACGTACGT", [(CIGAR_MATCH, 8)]) + aligned, inserts = build_read_row(read, 2, 6) + assert aligned == {2: "G", 3: "T", 4: "A", 5: "C"} + + def test_read_starting_after_window(self): + """Read fully outside the window produces empty results.""" + read = _mock_read("r1", 10, "ACGT", [(CIGAR_MATCH, 4)]) + aligned, inserts = build_read_row(read, 0, 5) + assert aligned == {} + assert inserts == {} + + def test_insertion_outside_window(self): + """Insertion anchored outside the window is not recorded.""" + # Query: ins(TT) A C G T + # CIGAR: 2I 4M at ref pos 0 + # Insertion anchor = -1 (before window start=0), so ignored. + read = _mock_read("r1", 0, "TTACGT", [(CIGAR_INS, 2), (CIGAR_MATCH, 4)]) + # Actually this insertion anchor is rpos-1 = 0-1 = -1 + aligned, inserts = build_read_row(read, 0, 4) + assert aligned == {0: "A", 1: "C", 2: "G", 3: "T"} + assert inserts == {} + + def test_multiple_insertions_at_same_position(self): + """Longer insertion produces multiple bases at the anchor.""" + # CIGAR: 1M 4I 1M at ref 0 + read = _mock_read( + "r1", 0, "ATTTTC", [(CIGAR_MATCH, 1), (CIGAR_INS, 4), (CIGAR_MATCH, 1)] + ) + aligned, inserts = build_read_row(read, 0, 2) + assert aligned == {0: "A", 1: "C"} + assert dict(inserts) == {0: ["T", "T", "T", "T"]} + + def test_complex_cigar(self): + """Mixed CIGAR: 3M 2I 1D 2M mimics a realistic read.""" + # Query: A C G ins(TT) _ A C + # CIGAR: 3M 2I 1D 2M, starting at ref 0 + read = _mock_read( + "r1", + 0, + "ACGTTAC", + [(CIGAR_MATCH, 3), (CIGAR_INS, 2), (CIGAR_DEL, 1), (CIGAR_MATCH, 2)], + ) + aligned, inserts = build_read_row(read, 0, 6) + assert aligned[0] == "A" + assert aligned[1] == "C" + assert aligned[2] == "G" + assert aligned[3] == "-" # deletion + assert aligned[4] == "A" + assert aligned[5] == "C" + assert dict(inserts) == {2: ["T", "T"]} + + def test_bases_uppercased(self): + """Lowercase query bases are converted to uppercase.""" + read = _mock_read("r1", 0, "acgt", [(CIGAR_MATCH, 4)]) + aligned, inserts = build_read_row(read, 0, 4) + assert aligned == {0: "A", 1: "C", 2: "G", 3: "T"} + + +# ── bam_panel integration tests ────────────────────────────────── +# These require pysam and indexed BAM files from examples/. + + +class TestBamPanel: + """Integration tests for bam_panel using example files.""" + + @pytest.fixture(autouse=True) + def _skip_if_no_pysam(self): + pytest.importorskip("pysam") + + def test_indel_bam_panel_shape(self): + """Panel from indel BAM has correct structure.""" + from tview.bam import bam_panel + + panel = bam_panel("examples/indel_sorted.bam", "examples/ref.fa", "chr1:0-50") + assert panel.label == "indel_sorted" + assert len(panel.ref_row) > 0 + assert len(panel.seq_rows) == 5 + assert panel.total_cols >= 50 + + def test_indel_bam_insertion_columns(self): + """Insertion columns are detected in the indel BAM.""" + from tview.bam import bam_panel + + panel = bam_panel("examples/indel_sorted.bam", "examples/ref.fa", "chr1:0-50") + assert len(panel.ins_columns) > 0 + + def test_reads_sorted_by_start(self): + """Reads in seq_rows are sorted by start position then strand.""" + from tview.bam import bam_panel + + panel = bam_panel("examples/indel_sorted.bam", "examples/ref.fa", "chr1:0-50") + # read5 is reverse-strand and should come last among reads starting at same position + names = [name for name, _, _ in panel.seq_rows] + assert "read5" in names + + def test_col_labels_start_at_one(self): + """Column labels are 1-based and start at position 1.""" + from tview.bam import bam_panel + + panel = bam_panel("examples/indel_sorted.bam", "examples/ref.fa", "chr1:0-50") + labels = [lbl for _, lbl in panel.col_labels] + assert labels[0] == "1" + + def test_sample2_bam(self): + """Second example BAM loads successfully.""" + from tview.bam import bam_panel + + panel = bam_panel("examples/sample2_sorted.bam", "examples/ref.fa", "chr1:0-50") + assert panel.label == "sample2_sorted" + assert len(panel.ref_row) > 0 diff --git a/tests/test_fasta.py b/tests/test_fasta.py index ef7c0ac..c2fe19f 100644 --- a/tests/test_fasta.py +++ b/tests/test_fasta.py @@ -607,6 +607,6 @@ def test_compose_with_matplotlib(self, tmp_path, output_dir): class TestPanel: def test_defaults(self): - p = Panel("test", ["A", "C"], [], 2, [], ins_columns=None) + p = Panel("test", ["A", "C"], [], 2, []) assert p.ins_columns == set() assert p.label == "test"