feat: support multiple BAM files with parallel processing

[ewels]

Summary

• Accept one or more BAM files as positional arguments to rustqc rna <BAM>... --gtf <GTF>
• When multiple BAMs are provided, they are processed in parallel using rayon, with threads distributed evenly across concurrent jobs
• The GTF annotation is parsed once and shared (read-only) across all parallel BAM processing jobs

Breaking Change

GTF moved from a positional argument to a --gtf / -g named flag to support variadic BAM inputs:

# Before
rustqc rna sample.bam annotation.gtf --outdir results

# After
rustqc rna sample.bam --gtf annotation.gtf --outdir results

# Multiple BAMs
rustqc rna sample1.bam sample2.bam sample3.bam --gtf annotation.gtf --outdir results --threads 12

Details

• Parallel processing: Multiple BAMs run concurrently via rayon par_iter. Thread allocation divides --threads evenly across parallel jobs (single BAM gets all threads).
• Duplicate stem detection: Rejects inputs where two BAM files share the same filename stem (e.g. dir1/sample.bam and dir2/sample.bam) since outputs would collide.
• Log clarity: All log messages prefixed with [bam_stem] when processing multiple BAMs.
• Error handling: If one BAM fails, remaining BAMs still complete. A summary of failures is reported at the end.

Files Changed

File	Change
src/cli.rs	bam → Vec<String>, gtf → --gtf flag, new unit test
src/main.rs	Parallel BAM dispatch, process_single_bam() extraction, duplicate detection
tests/integration_test.rs	Updated to --gtf flag, added multi-BAM and duplicate-stem tests
README.md	Updated CLI usage, examples, Docker, PGO, and performance docs
benchmark/README.md	Updated replication commands
AGENTS.md	Updated CLI syntax description
CHANGELOG.md	Added multi-BAM entry with breaking change note

Testing

• 35/35 tests pass (25 unit + 10 integration)
• cargo fmt --check clean
• cargo clippy -- -D warnings clean
• Manually verified with small benchmark (single + multiple BAMs)
• Manually verified with large 10GB benchmark (single + mixed parallel)