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In bash: cat test_389_JI.bed.gz test_390_JI.bed.gz > test_JI.bed.gz tabix -p bed test_JI.bed.gz
In Julia:
using GenomicFeatures
using BGZFStreams
JI_bed_reader = BED.Reader(BGZFStream("./test_JI.bed.gz"),
index = "./test_JI.bed.gz.tbi")
for i in eachoverlap(JI_bed_reader, Interval("chr6", 61374400, 61374500))
println(i)
end
ERROR: ArgumentError: too large in-block offset
Stacktrace:
[1] seek(::BGZFStream{IOStream}, ::VirtualOffset) at /nfs/users/nfs_r/ra11/.julia/packages/BGZFStreams/qApsr/src/bgzfstream.jl:225
[2] done(::GenomicFeatures.Indexes.TabixOverlapIterator{GenomicFeatures.BED.Reader}, ::GenomicFeatures.Indexes.TabixOverlapIteratorState{GenomicFeatures.BED.Record}) at /nfs/users/nfs_r/ra11/.julia/packages/GenomicFeatures/VNoux/src/indexes/overlap.jl:46
[3] iterate at /nfs/users/nfs_r/ra11/.julia/packages/GenomicFeatures/VNoux/src/indexes/overlap.jl:72 [inlined]
[4] iterate(::GenomicFeatures.Indexes.TabixOverlapIterator{GenomicFeatures.BED.Reader}) at /nfs/users/nfs_r/ra11/.julia/packages/GenomicFeatures/VNoux/src/indexes/overlap.jl:35
[5] top-level scope at ./REPL[5]:1
Expected Behavior
It shouldn't bring up that error. It should output intersected intervals just like tabix does.
Hitting error when analysing a bgzip BED that has been concatenated.
test_390_JI.bed.gz
test_389_JI.bed.gz
In bash:
cat test_389_JI.bed.gz test_390_JI.bed.gz > test_JI.bed.gz
tabix -p bed test_JI.bed.gz
In Julia:
Expected Behavior
It shouldn't bring up that error. It should output intersected intervals just like tabix does.
Current Behavior
produces the too large in-block offset error
Possible Solution / Implementation
Exclude the condition block.size = 0 & inblock_offset = 0 from the error check.
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