Regenerate legacy/genomes.json (restores mm10 and hg18 fasta index URLs)#5
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M4teuszzGl4dki wants to merge 1 commit into
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Regenerate legacy/genomes.json (restores mm10 and hg18 fasta index URLs)#5M4teuszzGl4dki wants to merge 1 commit into
M4teuszzGl4dki wants to merge 1 commit into
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Rebuilds the aggregate from genomes/legacy/json/ via scripts/buildGenomesJson.sh. Restores the fasta index URLs for mm10 and hg18, whose sources were fixed after this file was last built.
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The per-genome sources under
genomes/legacy/json/are correct, but the aggregategenomes/legacy/genomes.jsonhas not been rebuilt since they were last fixed, so two genomes still point at fasta indexes that 404.mm10.jsonwas fixed in 5f62c9a (2026-06-03 05:15Z), butlegacy/genomes.jsonwas last written in 85d606b at 03:43Z — about 1.5 hours earlier.hg18is stale in the same way.This PR is just the output of the existing build script, with no hand edits:
The regenerated file is byte-identical to the committed one apart from the two entries whose sources have since changed: the diff is +3/-3 lines, the file grows by exactly 15 bytes (3 × the 5 characters added to those paths), line endings are unchanged, and it still holds the same 42 entries in the same order. Nothing else moves.
Current status of the URLs involved (checked 2026-07-21):
igv.org/genomes/data/mm10.fa.fai(in the served file)igv.org/genomes/data/mm10/mm10.fa.fai(after this PR)igv.org/genomes/hg18/hg18.fasta[.fai](in the served file)igv.org/genomes/data/hg18/hg18.fasta[.fai](after this PR)This matters beyond the repo:
https://igv.org/genomes/genomes.json, which igv.js 2.x loads at startup, is currently byte-identical to this file. mm10 therefore fails to display in any igv.js 2.x embedding — that is how we ran into it (gladkia/igvShiny#107). Because the failing paths return no CORS headers, the browser reportsnet::ERR_FAILEDrather than a 404, which makes it look like a client bug.danRer11 and rn6 are broken in the same file but are not build staleness — their sources point at locations that are genuinely gone. Filed separately.