Complement Bed

# 3) Use a FASTA index as the genome file
complementBed \
  -i blacklist.bed \
  -g reference.fa.fai

Recommended Workflow

1. Build or obtain a correct genome file before trusting any complement output.
2. Make sure the interval file and genome file use the same chromosome names.
3. Decide whether the result should cover the whole genome from -g or only chromosomes that appear in the input (-L).
4. Inspect edge chromosomes manually when the complement is unexpectedly huge, because that often indicates naming mismatches or missing contigs.

Guardrails

• -g is mandatory.
• The genome file must be tab-delimited with chromosome name in column 1 and chromosome length in column 2.
• Without -L, chromosomes present in the genome file but absent from the input will be emitted in full as complement intervals.
• Complement assumes the input intervals represent covered regions; overlapping or unsorted input can still produce valid complement output, but upstream normalization is often wise.
• Prefer -h for help; wrapper behavior for --version is noisy.