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Add eof check

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The addition of an eof check appears to cover a corner case detailed at https://github.com/BioJulia/XAM.jl/issues/31#issuecomment-787480072.

# Conflicts:
#	src/bam/overlap.jl
This commit is contained in:
Ciarán O’Mara 2021-04-02 01:00:24 +11:00
parent 48ceb8d20e
commit f6e87dffa8
1 changed files with 4 additions and 1 deletions
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src/bam/overlap.jl
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@ -63,7 +63,10 @@ function Base.iterate(iter::OverlapIterator, state)
while state.chunkid ≤ lastindex(state.chunks)
chunk = state.chunks[state.chunkid]
while VirtualOffset(iter.reader.stream) < chunk.stop
read!(iter.reader, state.record)
if BioGenerics.IO.tryread!(iter.reader, state.record) === nothing
# no more overlapping records in this chunk since the end of the chunk was reached.
break
end
c = compare_intervals(state.record, (state.refindex, iter.interval))
if c == 0
return copy(state.record), state