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I believe this is really an issue with IGV.js and I've created an issue over there. But flagging here in case it isn't. Also, it's possible that the answer is "both", for instance if the solution is to upgrade to a new version of IGV.js.
Including the text from the iGV.js issue below:
We're using Quilt with IGV. It appears to be using version 2.5.11.
We noticed a set of our processed samples was failing to load the reference FASTA with the following error:
I looked into this saw that the fasta had a single contig named chr:1155232524-155232525. I was able to deterministically toggle the error by removing/re-adding the : in the contig name.
Examples that worked:
chrchr1155232524-155232525chr1 AC:CM000663.2 gi:568336023 LN:248956422 rl:Chromosome M5:6aef897c3d6ff0c78aff06ac189178dd AS:GRCh38foo
Examples that failed:
chr:1155232524-155232525chr:1-1000chr1:1-1000 AC:CM000663.2 gi:568336023 LN:248956422 rl:Chromosome M5:6aef897c3d6ff0c78aff06ac189178dd AS:GRCh38foo:something
Is this a known and/or expected issue?
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