Genomic intervals & annotation / BED sort and validate
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Intervals are sorted by chromosome and then by start; ties keep their original order. Several interval tools (closest feature, merge) expect sorted input.
“Lexicographic” matches the command-line sort -k1,1 (chr10 before chr2); “natural” orders the numeric part by value; you can also follow the order of a chromosome-length file (.fai) to match the reference genome.
The validation report lists malformed lines (too few columns, non-integer coordinates, end before start), zero-length intervals, exact duplicates, intervals overlapping the previous one and, with a length file, intervals beyond the chromosome end or on chromosomes missing from the file.
The bar chart shows intervals per chromosome; download the sorted result as CSV or copy the BED text.
Stable sort by chromosome and start; checked line by line against BEDTools sort (Quinlan & Hall 2010, Bioinformatics 26:841) and sort -k1,1V -k2,2n (records with equal starts are compared as groups, since the reference order of ties is not fixed).
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