All issues

Search results

gff3_file_to_proteins.pl gene mode picks the representative isoform at random — 1,991 of 43,981 genes lost when selecting primaries

Status: Open.

#30 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Aug 5, 2026

No pseudogene/retrocopy detection: miniprot Frameshift tags and neighbour-GFF exon structure are already generated but unused (_classify_discard is a residual label, not a test)

Status: Open.

#26 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 30, 2026

Filter.py: blank singleExon in the emitted tables is the multi-exon encoding, not a bug — filling it perturbs the RF feature space (-961 genes)

Status: Open.

#25 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 30, 2026

benchmark_busco: concurrent jobs race on the shared BUSCO lineage download — 4 of 10 labels failed on a corrupt tarball

Status: Open.

#24 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 30, 2026

OMArk silently produces empty results: shipped omark_db default points at a nonexistent file, and bundled omark 0.3.1 cannot read current OMAmer DBs

Status: Open.

#23 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 30, 2026

filterBlastP: homology evidence is circular when the protein DB contains the target species' own annotation (76% of best hits at 100% identity)

Status: Open.

#22 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 30, 2026

Dead/unwired bin modules carry verified defects (score_filter coverage reader, CombineDuck multi-source crash, exit-0-on-error) + RF-path test gap

Status: Open.

#21 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 24, 2026

P2 bundle: 12 Python correctness findings on the live DAG path (single-exon misclassification biases RF labels 3.3%, BUSCO-rescue gap, multi-parent feature loss, …)

Status: Open.

#20 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 24, 2026

P2 bundle: 12 shell/Snakefile robustness findings (runEVM masks mid-list EVM failures, recombineEVM absorbs strays, pasaPrep sed -i on input, …)

Status: Open.

#19 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 24, 2026

config_annotate.yml: 10+ more rules carry 4.91Gb-template resource requests (STAR_generate 200g, RepeatMasker 220g/64c, miniprot2genewise 128g/1cpu) — sacct-verified over-requests

Status: Open.

#18 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 24, 2026

merge_pasa_evm: multi-mapped EVM genes silently lost; tie handling contradicts docstring (EVM wins with zero evidence); gffread failures swallowed into ties

Status: Open.

#17 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 24, 2026

Snakefile_filter lacks set -euo pipefail strict mode (annotate-only rollout) — mid-block failures silently pass, e.g. zero-row coverage beds distort RF features

Status: Open.

#16 In plantgenomicslab/Sylvan;

· wyim-pgl opened on Jul 24, 2026