Sqanti reads plots

[carolinamonzo]

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[Copilot]

Pull request overview

This PR expands the SQANTI-reads feature set and regression coverage by adding extensive unit/integration tests for new QC/plot/report metrics, introducing a centralized YAML-configurable threshold system, and wiring new CLI options (including parallel per-sample jobs and a merged PDF/HTML reporting flow).

Changes:

• Add broad unit + integration test coverage for SQANTI-reads QC metrics, PDF page generation, and HTML report sections.
• Introduce src/utilities/sqanti_reads_config.py and a new --config CLI flag to override QC thresholds and other cutoffs.
• Add --jobs parallelization support and refine --refFasta/--skip_hash behavior in sqanti3_reads.py.

Reviewed changes

Copilot reviewed 38 out of 58 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
test/unit/utilities/test_ujc_overlap.py	Unit tests for A6 pairwise UJC overlap metric and PDF/HTML no-op behavior.
test/unit/utilities/test_transcript_divergency.py	Unit tests for transcript divergency computation and render guards.
test/unit/utilities/test_tandem_sites.py	Unit tests for tandem splice-site detector (F6) compute + rendering.
test/unit/utilities/test_support_views.py	Unit tests for orthogonal-support metrics (CAGE/polyA/SR) and pages.
test/unit/utilities/test_support_recommendation.py	Unit tests for “optional orthogonal support” messaging in PDF/HTML.
test/unit/utilities/test_scorecard_completeness.py	Unit tests for completeness + cohort-relative scorecard logic.
test/unit/utilities/test_replicate_concordance.py	Unit tests for replicate concordance (A5) compute + render guards.
test/unit/utilities/test_quality_metrics.py	Unit tests for derived quality scalars and cohort pages + scorecard feed.
test/unit/utilities/test_qc_pca.py	Unit tests for QC PCA feature selection and edge-case safety.
test/unit/utilities/test_jxn_yield.py	Unit tests for junction yield vs depth and scorecard flagging.
test/unit/utilities/test_jxn_fuzziness.py	Unit tests for splice-site fuzziness summarization/metrics/rendering.
test/unit/utilities/test_fuzziness_concordance.py	Unit tests for splice-site precision concordance and ref_key reconstruction.
test/unit/utilities/test_fuzz_depth.py	Unit tests for fuzziness vs junction depth (F4) compute + no-op behavior.
test/unit/utilities/test_composition_drift.py	Unit tests for composition drift (A3) compute + rendering + scorecard feed.
test/unit/utilities/test_artefact_pages.py	Unit tests for artefact cohort pages and HTML figure generation.
test/test_data/sqanti_reads/expected/sqantiReads_putative_underannotation.csv	Expanded expected under-annotation output fixture.
test/test_data/sqanti_reads/expected/sqantiReads_length_summary.csv	Expected length summary fixture.
test/test_data/sqanti_reads/expected/sqantiReads_gene_classfication.csv	Expected gene classification fixture.
test/test_data/sqanti_reads/design.csv	Design fixture (no factor).
test/test_data/sqanti_reads/design_with_upper_factor.csv	Design fixture to exercise uppercase factor name.
test/test_data/sqanti_reads/design_with_factor.csv	Design fixture (with factor).
test/test_data/sqanti_reads/design_single.csv	Design fixture for single-sample cohort behavior.
test/test_data/sqanti_reads/baseline/sqantiReads_putative_underannotation.csv	Baseline under-annotation regression oracle.
test/test_data/sqanti_reads/baseline/sqantiReads_length_summary.csv	Baseline length summary regression oracle.
test/test_data/sqanti_reads/baseline/sqantiReads_gene_classfication.csv	Baseline gene classification regression oracle.
test/test_data/genome/genome_test.fasta.fai	Genome index fixture for tests.
test/integration/test_sqanti_reads.py	End-to-end regression tests for merged report outputs, titles, HTML sections.
test/integration/conftest.py	Integration test runner for sqanti3_reads fast mode.
src/utilities/sqanti_reads_config.py	New centralized default config + YAML deep-merge loader.
src/reads_argparse.py	CLI updates: optional --refFasta, new --config, improved --skip_hash, new --jobs.
SQANTI3.conda_env.yml	Add plotly/pypdf/pymupdf; remove pdf2image; update env deps for tests/reporting.
sqanti3_reads.py	Parallel execution helper, conditional refFasta validation, skip_hash pathing, config/jobs plumbing.
pixi.toml	Add plotly/pypdf/pymupdf; remove pdf2image from pixi environment.
docs/Running-SQANTI‐reads.md	Update docs for new CLI, directory layout, report formats, config and new sections.
docs/commit_backlog.md	Add commit-backlog documentation file.
.gitignore	Ignore GEMINI.md.

Comments suppressed due to low confidence (1)

sqanti3_reads.py:308

• The paste step that writes {sample}_reads_classification.txt uses subprocess.call(...) and ignores failures. If this command fails (e.g., bash not available, process substitution disabled, disk full), the pipeline will continue with a missing/partial classification file and later steps may error in less obvious ways.

Use check_call (and ideally log the command) so the failure is caught at the source.

        cmd_paste = f"""bash -c 'paste <(cat {input_classfile} | tr -d '\r') <(cut -f 5,6 {outputPathPrefix}_temp.txt | tr -d '\r') > {outputPathPrefix}_reads_classification.txt'"""
        subprocess.call(cmd_paste, shell = True)

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