Integration/pr batch 1

[Psy-Fer]

integration/pr-batch-1: merge 14 open PRs + human-readable RAM params

Summary

Batch merge of 14 open PRs into an integration branch for combined testing before landing on main. Also extends --limitGenomeGenerateRAM and --limitBAMsortRAM to accept human-readable suffixes (64G, 512M, 1T).

Merged PRs (in order)

• feat(params): accept --limitGenomeGenerateRAM for STAR CLI compatibility #36 — --limitGenomeGenerateRAM CLI compatibility flag
• fix(chimeric): create output parent directory before writing #37 — Create chimeric output parent directory before writing
• fix(output): move pass-1 SJ tab into <prefix>_STARpass1/SJ.out.tab #44 — Move pass-1 SJ output to _STARpass1/SJ.out.tab
• fix(stats): route reads exceeding --outFilterMultimapNmax to too_many_loci counter #54 — Fix PE too_many_loci counter (n_for_mapq=0 bug)
• fix(bam): subtract Phred+33 offset from QUAL before writing to BAM #38 — Subtract Phred+33 offset from QUAL before writing to BAM
• fix(bam): emit SAM-spec NM:i: tag distinct from STAR-internal nM:i: #42 — Emit SAM-spec NM:i: distinct from STAR-internal nM:i:
• feat(bam): populate @PG header with PN/VN/CL fields #40 — Populate @PG header with PN/VN/CL fields
• fix(sjdb): key SpliceJunctionDb in genome-absolute 0-based coordinates #45 — Key SpliceJunctionDb in genome-absolute 0-based coordinates
• fix(stitch): use sjdb_score in place of motif_score on annotated junctions #52 — Use sjdb_score in place of motif_score on annotated junctions
• fix: decode Gsj-region SA hits into split splice seeds #51 — Decode Gsj-region SA hits into split splice seeds
• feat(bam): emit XS:A: strand tag when --outSAMstrandField intronMotif #43 — Emit XS:A: strand tag when --outSAMstrandField intronMotif
• fix(transcriptome-bam): write per-record RG:Z: tag matching @RG header #39 — Write per-record RG:Z: tag on transcriptome BAM
• fix(transcriptome-bam): populate mate fields on paired-end records #41 — Populate mate fields on PE transcriptome BAM records
• chore: switch sam attributes to bitflags #67 — Switch SAM attributes from HashSet<String> to bitflags (SamAttributes)
• fix(stats): route no-seeds-no-clusters reads to UnmappedReason::Other #49 — Confirmed already on main; closed without merge

Additional changes

• --limitGenomeGenerateRAM and --limitBAMsortRAM now accept human-readable memory values (64G, 512M, 1T, 1024, etc.) in addition to raw byte counts. Default changed to 31G. Tests added for both params.

Conflict resolutions

• feat(bam): emit XS:A: strand tag when --outSAMstrandField intronMotif #43 vs chore: switch sam attributes to bitflags #67 (params/mod.rs): HashSet<String> attribute methods removed; XS/intronMotif coupling baked into validate() — intronMotif adds XS, anything else strips it (matches STAR's final output behaviour regardless of input path).
• fix(bam): emit SAM-spec NM:i: tag distinct from STAR-internal nM:i: #42 vs chore: switch sam attributes to bitflags #67 (sam.rs): SamAttributes::NM bit covers both "NM" and "nM" CLI tokens; both NM:i: (edit distance) and nM:i: (mismatches-only) are emitted together when the bit is set.
• fix: decode Gsj-region SA hits into split splice seeds #51 (junction/mod.rs): Test struct literal updated to include new n_genome_real field added by fix: decode Gsj-region SA hits into split splice seeds #51.
• fix(transcriptome-bam): write per-record RG:Z: tag matching @RG header #39 (sam.rs): Test used undeclared CigarOp type alias; replaced with cigar::Op::new(cigar::op::Kind::Match, 4).

Test plan

• cargo test — 433 tests passing, 0 failures
• cargo clippy --all-targets — 0 warnings
• Run STAR faithfulness benchmark against yeast SE/PE test data
• Verify BAM QUAL scores with samtools stats (average_quality ~35, not ~68)
• Verify NM:i: tag present and correct with samtools view
• Verify XS:A: tag emitted when --outSAMstrandField intronMotif
• Verify splice count improvement from Gsj seeding (fix: decode Gsj-region SA hits into split splice seeds #51 + fix(sjdb): key SpliceJunctionDb in genome-absolute 0-based coordinates #45 + fix(stitch): use sjdb_score in place of motif_score on annotated junctions #52 combined)