Issues

• Detect: taxid 5158 has no NCBI lineage, and --phylum leaves MAT genes unmodelled (7 of 8 Ceratocystis fimbriata assemblies uncalled)

  stajichlab/MATPredict#324 · Filter by author hyphaltip opened on Nov 9, 2026

• Reads: linked-pair junction panel for active MAT (only if the ratio test fails its controls)

  stajichlab/MATPredict#323 · Filter by author hyphaltip opened on Nov 9, 2026 · v0.10.0

• Reads: copy-number ratio test for active MAT in cassette yeasts and MTL zygosity

  stajichlab/MATPredict#322 · Filter by author hyphaltip opened on Nov 9, 2026 · v0.10.0
  1

• Polish agreement test tolerates a junction difference that changes whether the model has a stop (Wallemia STE3)

  stajichlab/MATPredict#305 · Filter by author hyphaltip opened on Nov 8, 2026 · v0.10.0

• Defective-gene flag: per-species isolate count and table/site presentation (follow-up to #151)

  stajichlab/MATPredict#291 · Filter by author hyphaltip opened on Nov 7, 2026 · v0.10.0

• Use FungiDB annotations to check weak mating-type calls

  stajichlab/MATPredict#290 · Filter by author hyphaltip opened on Nov 7, 2026 · v0.9.0
  5

• Speed: two-stage search, cached records and the broad Basidiomycota cost (follow-up to #276)

  stajichlab/MATPredict#287 · Filter by author hyphaltip opened on Nov 7, 2026 · v0.9.0
  3

• Census of MAT1-1-1 introns and splice-site classes vs gene-predictor failures

  stajichlab/MATPredict#262 · Filter by author hyphaltip opened on Nov 5, 2026 · v0.10.0

• 12-locus sequence-level check before enabling the strong single-gene rule

  stajichlab/MATPredict#261 · Filter by author hyphaltip opened on Nov 5, 2026 · v0.9.0
  1

• Deep dive: CTG-clade yeasts that lost their MTLA1 polished model

  stajichlab/MATPredict#260 · Filter by author hyphaltip opened on Nov 5, 2026 · v0.10.0

• Plan for PyPI and bioconda distribution

  stajichlab/MATPredict#259 · Filter by author hyphaltip opened on Nov 5, 2026 · v0.10.0

• Cross-family tie-break: Basidiomycota locus loses its MAT alpha label to a PR call (GCA_017654745.1)

  stajichlab/MATPredict#255 · Filter by author hyphaltip opened on Nov 4, 2026 · v0.9.0
  2

• Curation: Taphrinomycotina MAT records for Saitoella, Protomyces and Neolecta

  stajichlab/MATPredict#202 · Filter by author hyphaltip opened on Oct 29, 2026 · v0.10.0

• Naming: nearest_reference column, NoRef loci and undetermined-allele counts

  stajichlab/MATPredict#200 · Filter by author hyphaltip opened on Oct 29, 2026 · v0.9.0
  1

• Reads: browser-side reads typing, timing test in Pyodide

  stajichlab/MATPredict#199 · Filter by author hyphaltip opened on Oct 29, 2026 · v0.10.0

• Reads: Basidiomycota raw-read typing, design (Cryptococcus a/alpha first)

  stajichlab/MATPredict#198 · Filter by author hyphaltip opened on Oct 29, 2026 · v0.10.0

• Reads: clone-aware reporting, open decisions and tests

  stajichlab/MATPredict#197 · Filter by author hyphaltip opened on Oct 29, 2026 · v0.10.0

• Reads: yeast panels (Saccharomyces sensu stricto, Candida albicans, Zygosaccharomyces, Lachancea and others) withheld in wave 2

  stajichlab/MATPredict#196 · Filter by author hyphaltip opened on Oct 29, 2026 · v0.9.0
  2

• Reads: species where presence of an idiomorph cannot be typed (silent cassettes, homothallic, switching) and what the gate should say

  stajichlab/MATPredict#195 · Filter by author hyphaltip opened on Oct 29, 2026 · v0.9.0
  2

• Reads: work list for the withheld filamentous and other non-yeast species (waves 1 and 2)

  stajichlab/MATPredict#194 · Filter by author hyphaltip opened on Oct 29, 2026 · v0.10.0

• Curate the 80 yeast genomes with a secondary-system MAT locus; Pichia has no reference record

  stajichlab/MATPredict#189 · Filter by author hyphaltip opened on Oct 28, 2026 · v0.10.0
  5

• Discovery: HMG-box and flank candidates for MAT loci in chytrids and other lineages with no known locus

  stajichlab/MATPredict#182 · Filter by author hyphaltip opened on Oct 28, 2026 · v0.10.0

• Raw-read MAT typing of public fungal population datasets (survey, panels, pipeline)

  stajichlab/MATPredict#173 · Filter by author hyphaltip opened on Oct 26, 2026 · v0.10.0
  5

• Landing page: show the Fola and A. fumigatus read-typing results like Coccidioides (charts, per-strain tables)

  stajichlab/MATPredict#172 · Filter by author hyphaltip opened on Oct 26, 2026 · v0.9.0
  2

• Basidiomycota: 14 MAT-family loci outside Tremellomycetes rest on STE3 plus PAN6 or RPL39

  stajichlab/MATPredict#170 · Filter by author hyphaltip opened on Oct 26, 2026 · v0.9.0
  1