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Colons in contig names appear to cause rendering error #1941

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geoffjentry opened this issue Feb 22, 2025 · 0 comments
Open

Colons in contig names appear to cause rendering error #1941

geoffjentry opened this issue Feb 22, 2025 · 0 comments

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@geoffjentry
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geoffjentry commented Feb 22, 2025

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:

Image

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:

  1. chr
  2. chr1155232524-155232525
  3. chr1 AC:CM000663.2 gi:568336023 LN:248956422 rl:Chromosome M5:6aef897c3d6ff0c78aff06ac189178dd AS:GRCh38
  4. foo

Examples that failed:

  1. chr:1155232524-155232525
  2. chr:1-1000
  3. chr1:1-1000 AC:CM000663.2 gi:568336023 LN:248956422 rl:Chromosome M5:6aef897c3d6ff0c78aff06ac189178dd AS:GRCh38
  4. foo:something

Is this a known and/or expected issue?

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