Details
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Type: Improvement
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Status: In Progress
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Priority: Major
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Resolution: Unresolved
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Affects Version/s: 2.10.3, 2.10.4
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Fix Version/s: 2.11.1_js
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Component/s: file format issue
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Labels:None
Description
Certain tools don't produce GFF files with properly formatted headers, e,g,
#gff-version 3
...
In this situation, Jalview behaves confusingly, attempting to parse the file as a Jalview features file, but then failing to annotate sequences because Jalview's feature format has the sequence ID in column 2 rather than column 1 (as in GFF).
Recommend patching the parser to detect gff pragmas beginning with only one '#'.
#gff-version 3
...
In this situation, Jalview behaves confusingly, attempting to parse the file as a Jalview features file, but then failing to annotate sequences because Jalview's feature format has the sequence ID in column 2 rather than column 1 (as in GFF).
Recommend patching the parser to detect gff pragmas beginning with only one '#'.