feat: --chimOutJunctionFormat (STAR-Fusion comment trailer) - #128
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BenjaminDEMAILLE wants to merge 1 commit into
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feat: --chimOutJunctionFormat (STAR-Fusion comment trailer)#128BenjaminDEMAILLE wants to merge 1 commit into
BenjaminDEMAILLE wants to merge 1 commit into
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Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
--chimOutJunctionFormat:0(plain, default) or1(append a STAR-Fusion-style comment trailer toChimeric.out.junctionafter all junction lines: a# <version> <command line>header, then# Nreads .. NreadsUnique .. NreadsMulti ..counts).--chimFilter banGenomicNrequires 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/--chimNonchimScoreDropMinare a genuinely separate, larger feature (full multimap chimeric detection with extra output columns), not a config knob on existing behavior.Test plan
cargo fmt --checkcargo clippy --workspace --all-targets -- -D warnings(0 warnings)cargo test --workspace(456 passed, incl. newtest_chim_out_junction_format1_trailer)Chimeric.out.junctiongets the junction line plus the two trailer comment lines (version/command-line, thenNreads 1 NreadsUnique 1 NreadsMulti 0) with--chimOutJunctionFormat 1