# Real-genome oriC regression truth for oricle.
#
# Coordinates are DoriC (https://tubic.org/doric/) origins, re-derived on the
# CURRENT RefSeq accession version by exact-matching each DoriC oriC sequence
# against the genome (DoriC stores coordinates against older accession versions,
# so its stated numbers can be kilobases off). The E. coli entry additionally
# agrees with NCBI's own `rep_origin` annotation (3925744..3925975).
#
# Columns: accession oric_start oric_end topology tolerance_bp note
# tolerance_bp is the max allowed distance from the predicted region to this
# interval for the regression to pass. Origins that wrap coordinate 1 have
# start > end.
#
# To run: ORICLE_GENOME_DIR=/path/to/fastas cargo test --test regression -- --nocapture
# where the dir holds <accession>.fa (or .fasta/.fna) FASTA files. A dnaA gene
# hint TSV (<accession>.genes.tsv: seqname start end name) is used if present.
NC_000913.3 3925634 3926011 circular 5000 E. coli K-12 MG1655; NCBI rep_origin inside
NC_000964.3 4215390 409 circular 5000 B. subtilis 168; wraps origin
NC_002516.2 6264362 482 circular 5000 P. aeruginosa PAO1; wraps origin
NC_007795.1 1879 2155 circular 5000 S. aureus NCTC8325
NC_003210.1 2944342 317 circular 5000 L. monocytogenes EGD-e; wraps origin
NC_009089.1 1321 1561 circular 8000 C. difficile 630
NC_002505.1 2961047 234 circular 8000 V. cholerae chr1; wraps origin
NC_003888.3 4269844 4270777 linear 8000 S. coelicolor A3(2); linear, needs dnaA hint
NC_000962.3 1525 2051 circular 8000 M. tuberculosis H37Rv (biologically circular)