Covers the conventions that produce silent off-by-one and wrong-assembly
errors: 0-based half-open vs 1-based inclusive across BED/GFF/VCF/SAM and
friends, VCF indel anchoring and left-alignment, GRCh37 vs hg19 vs GRCh38
vs T2T, and genomic-to-transcript-to-CDS-to-protein positions.
Four standard-library scripts, no network:
- convert_coords.py intervals between 21 conventions
- normalize_variant.py trim and left-align against a reference, compare
two representations for equivalence
- check_contigs.py identify the assembly, report why two files
will not join
- audit_intervals.py scan a BED/GTF/GFF3/VCF for convention violations
Build signatures are read from the UCSC chrom.sizes files and the NCBI
GRCh37.p13 assembly report; region-string semantics follow the samtools
manual, including that REF:START runs to the end of the contig and that
GRCh38 HLA contig names need htslib brace quoting.
ce67928122