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Adjust BGZFStreams.virtualoffset

Browse source 
https://github.com/BioJulia/BGZFStreams.jl/issues/22#issuecomment-874491338
This commit is contained in:
Ciarán O’Mara 2021-05-16 12:20:55 +10:00
parent 0e6ef62e3e
commit 7443237129
1 changed files with 16 additions and 0 deletions
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16
src/bam/bam.jl
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@ -15,6 +15,22 @@ import BioGenerics: isfilled, header
import GenomicFeatures: eachoverlap
# Overwrite virtualoffset method as per https://github.com/BioJulia/BGZFStreams.jl/issues/22#issuecomment-874491338.
function BGZFStreams.virtualoffset(stream::BGZFStreams.BGZFStream)
if stream.mode == BGZFStreams.READ_MODE
i = BGZFStreams.ensure_buffered_data(stream)
if i == 0
# Provide a VirtualOffset beyond the bounds of the stream.
block = stream.blocks[end]
return BGZFStreams.VirtualOffset(block.block_offset, 0) + (block.position - 1)
else
block = stream.blocks[i]
end
else
block = stream.blocks[1]
end
return BGZFStreams.VirtualOffset(block.block_offset, block.position - 1)
end
include("bai.jl")
include("auxdata.jl")