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Tracking: PRs for #31, #95, #172, #218, #223, #270, #279, #280

Aperta
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Valutazione

Difficoltà
5/5
Tempo stimato
Più di una settimana
Idoneità per principianti
10/100
Tipo di issue
Funzionalità
Chiarezza
Da chiarire
Stato di attività
Ferma
Stack tecnologico
rust
Ambito
bioinformatics

Direzione di ricerca

Start with the PR and checklist table, then review the referenced issues and PRs such as #272, #273, #274, #276, #278, #281, and #282. Done means the listed PRs and dependencies are resolved, open design and maintainer-sign-off points are decided, and the remaining conflicts and benchmark gaps are addressed.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Tracking the batch of PRs opened for the six open issues that had no PR or assignee, plus two bugs found along the way (#279, #280).

PRs

Issue PR Status Closes issue?
#31 NH cap vs STAR #271 Ready for review. Stacked on #254 (base fix/pair-subset-loci), adds a same chromosome/strand guard Via #254
#218 bz2/zstd/xz input #272 Ready for review Yes
#95 paraseq input #273 Ready for review Yes
#172 solo CellRanger flags #274 Ready for review Partially (Refs)
#270 hdf5-pure .h5 output #275 Proposal, design open No (Refs)
#223 thread scaling #276 Ready for review (parallel BGZF compression) No (Refs)
#223 thread scaling #278 Ready for review. Stacked on #276: SAM/BAM record encoding on the align workers, gated on core saturation With #276, yes
#279 SE WithinBAM crash #282 Ready for review. STAR hard-clip rules for SE supplementary records Yes
Bulk total RNA (unspliced targets) #283 Ready for review. Opt-in <gene_id>-I targets in TranscriptomeSAM, sp tag, GeneSplicing table; fixes a TranscriptomeSAM soft-clip crash n/a (Refs COMBINE-lab/salmon#1229)
#280 per-read 10k reservation #281 Ready for review. Peak RSS ~8x lower, 6-17% faster Yes

Checklist

  • #254 then #271 (#31)
  • #272 (#218)
  • #273 (#95), after #272
  • #274 (#172)
  • #275 (#270)
  • #276 (#223, parallel BGZF compression)
  • #278 (#223, parallel record encoding), after #276
  • #282 (#279)
  • #281 (#280)
  • #283 (bulk total RNA, needs maintainer sign-off on non-STAR flags)

Suggested merge order and known conflicts

  1. #219 / #225 vs #272: all three touch the gzip branch of src/io/fastq.rs. #272 already uses MultiGzDecoder (keep its version over #219's; #219's solo fixes are still needed). #225's rapidgzip call moves into the Gzip arm of src/io/compression.rs. #272 and #225 both add a [features] table to Cargo.toml.
  2. #273 after #272: paraseq should read from #272's open_decoded so it inherits format detection and multi-member gzip.
  3. #274 vs #165: #274 supersedes the cbMinP / oneExact part of #165. Conflicts in resolve_multi_cb and CHANGELOG.md.
  4. #275 vs #237: trivial conflict in src/lib.rs next to write_gene_matrix. Different flag and feature (--soloOutH5 / hdf5-out vs --soloOutputFormat / anndata-out).
  5. #276: independent of #222, #261, #225, #211, #259. #278 (stacked on #276): simulated 3-way merge of src/lib.rs against #222 and #261 gives 0 conflicts.

Open points

  • #218 / #272: behaviour change needs maintainer sign-off. Input compression is detected from content, so a plain *.gz file is read as plain text. The STAR citation in DIVERGENCE.md §4.3 needs a check.
  • #172 / #274: the 8.9% matrix gap has not been re-measured (needs STAR and the 20k-read fixture). Known remaining gaps: CellReads.stats counts reads later dropped by oneExact; Transcript3p records are not filtered by oneExact.
  • #270 / #275: is there a consumer for .h5 (scanpy, Seurat and CellBender read the MTX directory)? Should it become a --soloOutputFormat value once #237 lands?
  • #31 / #271: the strand guard was not re-benchmarked on the #31 fixture.
  • #223 / #278: pre-encoding is gated (on only when runThreadN nearly covers all cores) because it is slower at low thread counts. RUSTAR_PRE_ENCODE=0|1 overrides.
  • #279 / #282: remaining STAR differences in WithinBAM: normal alignment still written alongside the chimera, several chimeras per read possible, PE records lack mate fields and hard clips, QUAL empty.
  • #281 vs #278: both touch BufferedSamRecords (#278 adds fields), minor conflict.
  • #95 / #273: paraseq rejects records whose sequence and quality lengths differ (noodles accepts them). Malformed input only.

🤖 Generated with Claude Code

Lingua principale
Rust
Stelle
90
Fork
9
Merge medio
21h 12m
PR unite (30g)
21

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