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Report has value "Unknown" for assembly in VIP 5.2 #120

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bartcharbon opened this issue Mar 31, 2023 · 1 comment
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Report has value "Unknown" for assembly in VIP 5.2 #120

bartcharbon opened this issue Mar 31, 2023 · 1 comment
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Report has value "Unknown" for assembly in VIP 5.2.0
@dennishendriksen dennishendriksen added the bug Something isn't working label Apr 17, 2023
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The default molgenis/vip-report-template displays the value of the assembly field returned by api.getHtsFileMetadata(). molgenis/vip-report populates this field using org.molgenis.vcf.utils.sample.mapper.HtsFileMapper from molgenis/vip-utils which tries to extract the assembly value from the 1.4.6 Assembly field.

According to this specification this field is meant for Breakpoint assemblies for structural variations may use an external file and the value is an url from which follows that the current implementation is using the wrong field.

Since the assembly is not stored in the input .vcf and is not passed as a command-line argument to vip-report the value Unknown is correct.

This was referenced Sep 12, 2023
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@dennishendriksen @bartcharbon