Automate a repeat annotation pipeline

This tool runs RepeatModeler, curates each discovered repeat family against the genome, and then runs RepeatMasker.

The curation stage:

1. Builds a nucleotide BLAST database from the staged genome.
2. Searches the RepeatModeler consensi.fa.classified library against it.
3. Keeps the 20 best hits per family, merges nearby fragments, and adds 2 kb flanks.
4. Reverse-complements regions whose hits are predominantly on the minus strand.
5. Writes per-family FASTA files and MAFFT alignments under curation/.

Required executables are resolved from PATH. Custom installations can be selected with:

• REP_REPEATMASKER
• REP_REPEATMODELER
• REP_BUILD_DATABASE
• REP_MAKEBLASTDB
• REP_BLASTN
• REP_MAFFT

Use --curation_target <FASTA> to search the RepeatModeler consensus against a different genome; gzip-compressed targets are decompressed into the curation workspace. Use --curation_only to resume curation from an existing RepeatModeler output without rerunning discovery.

The Rust API also exposes CurationConfig and run_curation_with_config to customize flank length, maximum hit distance, orientation threshold, and hits per query.