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gffstring merges multi-position features #15

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ian-small opened this issue Nov 12, 2024 · 1 comment
Closed

gffstring merges multi-position features #15

ian-small opened this issue Nov 12, 2024 · 1 comment

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@ian-small
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julia> test_locus = Join([ClosedSpan(1:10), ClosedSpan(20:30)])
join(1..10,20..30)
julia> test_locus.position isa Vector
false
julia> typeof(test_locus.position)
Base.Iterators.Flatten{Base.Generator{Vector{SpanLocus{ClosedSpan}}, GenomicAnnotations.var"#24#25"}}

Thus 'if locus(gene).position isa Vector' in gffstring() fails and the feature is written to the .gff file as a single span from 1:30
This messes up CDS features with introns, for example.
Is this a bug, or am I creating my Joins wrongly?

@kdyrhage
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That is indeed a bug. I will update gffstring so that it works with the v0.4 loci representation.

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