feat: add SAM and CRAM input support

[ewels]

Summary

• Add support for SAM and CRAM input files alongside the existing BAM support (rust-htslib auto-detects format)
• Add --reference / -r CLI option for specifying a CRAM reference FASTA, with early validation when missing
• Update all CLI help text, error messages, log output, and documentation to be format-agnostic

Changes

CLI (src/cli.rs)

• Rename bam positional argument to input (accepts SAM/BAM/CRAM)
• Add --reference / -r option for CRAM reference FASTA

Core (src/counting.rs)

• Thread reference: Option<&str> through count_reads() and process_chromosome_batch()
• Call set_reference() on all htslib readers when a reference is provided
• Update error/log messages and doc comments to say "alignment file" instead of "BAM"

Entry point (src/main.rs)

• Early validation: bail with a clear message if CRAM input is detected without --reference or REF_PATH env var
• Rename bam_stem → input_stem, update log messages

Config (src/config.rs)

• Rename bam_to_gtf_mapping() → alignment_to_gtf_mapping()

Tests

• New SAM integration test (test_sam_input_matches_bam) verifying identical output to BAM
• New tests/data/test.sam test fixture
• --reference flag coverage in CLI unit test

Documentation

• README: new "Supported Formats" section, updated usage examples
• CHANGELOG, CONTRIBUTING, benchmark README updated