Log.out and Log.progress.out

[Psy-Fer]

feat: write Log.out and Log.progress.out

Closes #55.

Summary

rustar-aligner was writing only Log.final.out. STAR writes two additional log files that
pipeline tools (nf-core/rnaseq, MultiQC, custom QC dashboards) consume for provenance,
progress monitoring, and run validation. Both files are now written with real content —
not stubs or debug dumps.

Files written

Log.out — mirrors STAR's verbose run log:

• Version header (STAR version=, compilation time)
• Full command line as invoked
• Three parameter sections in STAR's format:
  • ##### Initial USER parameters from Command Line
  • ###### All USER parameters from Command Line (with ~RE-DEFINED markers)
  • ##### Final user re-defined parameters + reconstructed effective command line
• Chromosome table (index name length start — real values from the loaded genome)
• Phase timestamps: "Started/Finished loading the genome" and "..... finished mapping"
• ALL DONE!

Log.progress.out — mirrors STAR's periodic alignment progress log:

• STAR's exact two-line column header
• One final summary line with real counts: elapsed time, speed (M reads/hr), total reads,
  average read length, unique mapped, average mapped length, multi-mapper rate, multi count,
  mismatch-filtered, too-short, and other unmapped
• ALL DONE!

Implementation

New module src/io/log.rs with two public functions:

• write_log_out(path, params, genome, time_start, time_genome_loaded, time_finish)
• write_log_progress_out(path, stats, time_start, time_finish)

cli_params() helper parses params.command_line (already captured for the @PG BAM
header by PR #40) into (name, value) pairs for the parameter sections.

lib.rs changes:

• Added time_genome_loaded timestamp immediately after GenomeIndex::load
• Calls both writers after Log.final.out at the end of align_reads

Test plan

• cargo test — 434 tests passing, 0 failures
• cargo clippy --all-targets — 0 warnings
• cargo fmt --check — clean
• SE benchmark: 8604/8926 (96.4%) — unchanged
• PE benchmark: 8390/8390 both-mapped — unchanged
• Manual smoke-test: all three Log*.out files present in output directory; Log.out
  contains real command line, chromosome table, and ALL DONE!; Log.progress.out
  contains STAR header, a stats line with real read counts, and ALL DONE!