Issues · scverse/rustar-aligner · GitHub

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`--chimSegmentMin > 0` + `--twopassMode Basic` aborts the run when `--outFileNamePrefix` doesn't end in `/`

#35

· pinin4fjords opened

on May 12, 2026

BAM `QUAL` field is offset by +33 (Phred+33 ASCII bytes written instead of raw Phred values)

#34

· pinin4fjords opened

on May 12, 2026

BAM fidelity gaps: content-free `@PG` header line + `AS:i:` values disagree on identical-CIGAR records

#33

· pinin4fjords opened

on May 12, 2026

Transcriptome BAM (`--quantMode TranscriptomeSAM`) omits per-record `RG:Z:` tag

#32

· pinin4fjords opened

on May 12, 2026

Multi-mapper NH cap differs from STAR (NH up to 20 vs STAR's 7); possibly missing `--outFilterMultimapScoreRange`

#31

· pinin4fjords opened

on May 12, 2026

`--outSAMstrandField intronMotif` does not produce any `XS:A:` tags

#30

· pinin4fjords opened

on May 12, 2026

`--outSAMattributes NM` emits `nM:i:` instead of `NM:i:` (SAM-spec NM tag missing)

#29

· pinin4fjords opened

on May 12, 2026

STAR drop-in: output-shape gaps (`Log.out` / `Log.progress.out` missing, `SJ.pass1.out.tab` at top level)

#28

· pinin4fjords opened

on May 12, 2026

`Log.final.out` always reports `Number of splices: Annotated (sjdb) = 0` despite `--sjdbGTFfile`

#27

· pinin4fjords opened

on May 12, 2026

`--outFileNamePrefix` ending in `.` is treated as a directory (STAR uses it as a literal string prefix)

#26

· pinin4fjords opened

on May 12, 2026

`--limitGenomeGenerateRAM` rejected at CLI parser (STAR-compat regression)

#25

· pinin4fjords opened

on May 12, 2026

`--quantMode TranscriptomeSAM` paired-end BAM omits mate fields, breaking Salmon TPMs

#22

· pinin4fjords opened

on May 12, 2026