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Add CHM13 genome #14

Merged
merged 3 commits into from
May 3, 2023
Merged

Add CHM13 genome #14

merged 3 commits into from
May 3, 2023

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serge-p7v
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I also had to make gaps URL nullable because the new version of human genome doesn't have any gaps.

Sergey Pestrikov added 2 commits March 23, 2023 12:50
@serge-p7v serge-p7v requested a review from olegs April 5, 2023 13:44
@serge-p7v serge-p7v self-assigned this Apr 5, 2023
@serge-p7v
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Unfortunately, there are 124 warnings in the log such as:
2023-04-05 15:42:24,732 WARN [main] o.j.b.g.GtfReader [Ensembl.kt:337] Cannot detect UTR3 5' end for CHM13_T0140831. Not enough space for STOP codon only 1 bp available in exons after CDS 3' end.

That might be due to the problems in GTF file. The related issues are:
marbl/CHM13#52
ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit#285

@iromeo
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iromeo commented Apr 18, 2023

I think it will be useful to AnnotationsConfigLoaderTest.parseYaml() to ensure that the genome with missing gap information can be successfully loaded from the YAML config. I suggest just updating test_annotations.yaml with config close to CHM13 genome.

@serge-p7v
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Thank you! I've just added the hs1 to test_annotations.yaml and updated the test.

@olegs olegs merged commit 25ab66a into master May 3, 2023
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3 participants