feat(utils): Ensure reference first in alignment#31
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This pull request adds robust handling to ensure that the reference genome is always the first sequence in the alignment FASTA file, which is required by the
faToVcftool. It introduces a new utility function.fixes #30
Core functionality and CLI integration:
ensure_reference_is_first_in_alignmentinbarcodeforge/utils.pyto guarantee the reference genome is the first sequence in the alignment. This function checks, prepends, or deduplicates as needed, and handles errors for empty alignments or length mismatches.ensure_reference_is_first_in_alignmentinto thebarcodeCLI command to ensure downstream tools always receive a correctly ordered alignment. [1] [2]