fix(params): treat --outFileNamePrefix as a literal string prefix

[pinin4fjords]

Summary

--outFileNamePrefix SAMPLE. (or any value not ending in /) was treated as a directory by rustar - outputs landed in SAMPLE./Aligned.out.bam etc. STAR concatenates the prefix straight onto each output filename: SAMPLE.Aligned.out.bam at the top level. Every STAR wrapper assumes the latter convention; the directory behaviour breaks the output-glob convention nf-core/rnaseq and most STAR Snakemake wrappers rely on.

Root cause: out_file_name_prefix was typed as PathBuf and joined via .push("Aligned.out.bam"). That always treats the existing value as a directory component.

Fix

Change the type to String and concatenate at every output-write site:

// before:
let mut path = PathBuf::from(&params.out_file_name_prefix);
path.push("Aligned.out.bam");

// after:
let path = PathBuf::from(format!("{}Aligned.out.bam", params.out_file_name_prefix));

A small Parameters::output_path("Aligned.out.bam") helper does this concatenation once so the call sites stay readable. The chimeric junction writer (which already took the prefix as &str) was using PathBuf::push internally and is fixed the same way.

Trailing-slash prefixes (out/) still work - format! produces out/Aligned.out.bam, a valid path. The bare-dot case now produces SAMPLE.Aligned.out.bam at the top level, matching STAR.

Test plan

• New unit tests on Parameters::output_path cover bare-dot, trailing-slash, default, and path-with-underscore prefixes
• New integration test test_bare_dot_prefix_is_literal_string runs the binary with <run_dir>/SAMPLE. and asserts SAMPLE.Aligned.out.bam + SAMPLE.Log.final.out land at the top level and that no SAMPLE./ directory is created
• New chimeric writer unit test test_chimeric_junction_writer_bare_dot_prefix covers the same case for Chimeric.out.junction
• Existing integration tests (tests/alignment_features.rs, tests/phase9_threading.rs, tests/transcriptome_sam.rs) all already use trailing-slash prefixes and continue to pass unchanged
• cargo build
• cargo clippy --lib -- -D warnings
• cargo fmt --check
• cargo test - all 402 tests pass (388 lib + 9 alignment_features + 4 phase9_threading + 1 transcriptome_sam)

After this fix, no downstream wrapper needs the workaround that flattens SAMPLE./ back to STAR-style filenames after the run.

Fixes #26

[pinin4fjords]

Verified end-to-end on macOS/aarch64 against the rebuilt fix branch.

Bare-dot prefix (--outFileNamePrefix SAMPLE.) - the issue's failure case:

$ ls SAMPLE.*
SAMPLE.Aligned.out.bam
SAMPLE.Log.final.out
SAMPLE.SJ.out.tab
SAMPLE.SJ.pass1.out.tab

$ [ -d "SAMPLE." ] && echo dir-exists || echo no-dir
no-dir

Top-level SAMPLE.Aligned.out.bam, SAMPLE.Log.final.out, SAMPLE.SJ.out.tab all land, matching STAR's literal-string-prefix convention. No SAMPLE./ directory created.

Trailing-slash prefix (--outFileNamePrefix outdir/) - regression check:

$ ls outdir/
Aligned.out.bam
Log.final.out
SJ.out.tab
SJ.pass1.out.tab

Still produces files inside the directory as expected; the fix didn't regress the directory-style usage.

LGTM.