feat(bam): emit XS:A: strand tag when --outSAMstrandField intronMotif

[pinin4fjords]

Summary

--outSAMstrandField intronMotif was a no-op at tag-write time - accepted at the CLI parser, but the output BAM contained zero XS:A: tags. Downstream tools that need strand inference (StringTie, Cufflinks, rseqc infer_experiment.py) saw nothing.

samtools view <bam> | grep -c 'XS:A:' pre-fix: 0. STAR on the same data: 1 738.

Fix

Mirror STAR's two coupling paths from Parameters_samAttributes.cpp:

1. XS in --outSAMattributes -> force outSAMstrandField = intronMotif and add XS to the effective attribute set (lines 172-179).
2. --outSAMstrandField intronMotif (regardless of --outSAMattributes) -> add XS to the effective attribute set (lines 213-216).

Per-record write: map Transcript::junction_motifs to a strand char (canonical GT/AG donor -> +, canonical CT/AC -> -, non-canonical or mixed -> omit). Emitted alongside the existing NH / HI / MD tags wherever a record is built.

The motif detection itself is already implemented (src/align/score::SpliceMotif, Transcript::junction_motifs); this PR just plumbs the existing data into the tag write.

Test plan

• Unit test: --outSAMstrandField intronMotif adds XS to the effective attribute set
• Unit test: --outSAMattributes XS force-enables intronMotif strand inference
• Unit test: motif-to-strand mapping (canonical fwd → +, canonical rev → -, non-canonical → None)
• Integration-style test: spliced record with a canonical motif produces XS:A:+ in the emitted record
• cargo build / cargo clippy --lib -- -D warnings / cargo fmt --check

After this fix, samtools view <bam> | grep -c 'XS:A:' returns a positive count on spliced data, and infer_experiment.py no longer reports "stranding could not be inferred".

Fixes #30

[pinin4fjords]

Verified end-to-end on macOS/aarch64 against the rebuilt fix branch with --outSAMstrandField intronMotif and NO explicit XS in --outSAMattributes:

$ samtools view <bam> | grep -c 'XS:A:'    -> 549
$ samtools view <bam> | grep -oE 'XS:A:[+-]' | sort | uniq -c
    378  XS:A:+
    171  XS:A:-

Pre-fix the same invocation produced 0 XS:A: tags. The coupling works — --outSAMstrandField intronMotif alone is enough to populate the tag, no explicit XS in --outSAMattributes required.

Sample spliced records (all spliced records on long introns have XS populated):

SRR6357072.23987692  61M366N40M    XS:A:+
SRR6357072.11621763  8S83M11893N10M  XS:A:+
SRR6357072.36219571  87M11893N13M1S  XS:A:+

The total count (549) is lower than STAR's 1738 on the same data, but that gap is downstream of #27 (~50 % fewer spliced reads in rustar overall on this profile) plus the mixed-motif omit-XS policy — not a hole in the XS-tag fix itself.

LGTM.