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feat: --chimOutJunctionFormat (STAR-Fusion comment trailer) - #128

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BenjaminDEMAILLE wants to merge 1 commit into
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BenjaminDEMAILLE:bd/chim-config
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feat: --chimOutJunctionFormat (STAR-Fusion comment trailer)#128
BenjaminDEMAILLE wants to merge 1 commit into
scverse:mainfrom
BenjaminDEMAILLE:bd/chim-config

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Summary

  • Adds --chimOutJunctionFormat: 0 (plain, default) or 1 (append a STAR-Fusion-style comment trailer to Chimeric.out.junction after all junction lines: a # <version> <command line> header, then # Nreads .. NreadsUnique .. NreadsMulti .. counts).
  • Scoped out of this PR (deferred, needs more study before touching): --chimFilter banGenomicN requires retrofitting a genomic-N junction-rejection check into rustar-aligner's chimeric breakpoint placement, which is structurally simpler than STAR's exhaustive ambiguous-breakpoint search that the check is normally embedded in — risks silently changing which junction position gets chosen. --chimMultimapNmax / --chimMultimapScoreRange / --chimNonchimScoreDropMin are a genuinely separate, larger feature (full multimap chimeric detection with extra output columns), not a config knob on existing behavior.

Test plan

  • cargo fmt --check
  • cargo clippy --workspace --all-targets -- -D warnings (0 warnings)
  • cargo test --workspace (456 passed, incl. new test_chim_out_junction_format1_trailer)
  • Manual smoke test: synthetic two-chromosome genome + a chimeric read spanning both, confirmed Chimeric.out.junction gets the junction line plus the two trailer comment lines (version/command-line, then Nreads 1 NreadsUnique 1 NreadsMulti 0) with --chimOutJunctionFormat 1

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@Psy-Fer Psy-Fer mentioned this pull request Jul 25, 2026
@Psy-Fer Psy-Fer closed this Jul 25, 2026
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2 participants