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chore: Update GenomicFeatures to v3 #10

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chore: Update GenomicFeatures to v3 #10

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9a3f1dc
chore: Update GenomicFeatures compat bounds to v3
MillironX May 23, 2023
77a173a
chore: Change Interval references to GenomicInterval
MillironX May 23, 2023
c5abbde
chore: Change seqname(::GenomicInterval) references to groupname
MillironX May 23, 2023
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2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
[compat]
BioGenerics = "0.1"
CodecBGZF = "0.1"
GenomicFeatures = "2"
GenomicFeatures = "3"
TranscodingStreams = "0.9.5"
julia = "1.3"

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2 changes: 1 addition & 1 deletion src/Indexes.jl
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Expand Up @@ -12,7 +12,7 @@ using TranscodingStreams

import CodecBGZF
import BioGenerics
import GenomicFeatures: Interval
import GenomicFeatures: GenomicInterval

include("chunk.jl")
include("bgzfindex.jl")
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4 changes: 2 additions & 2 deletions src/overlap.jl
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Expand Up @@ -3,7 +3,7 @@

struct TabixOverlapIterator{T}
reader::T
interval::Interval
interval::GenomicInterval
end

function Base.eltype(::Type{TabixOverlapIterator{T}}) where T
Expand Down Expand Up @@ -76,7 +76,7 @@ function Base.iterate(iter::TabixOverlapIterator, state)
end

function icmp(record, interval)
c = cmp(BioGenerics.seqname(record), BioGenerics.seqname(interval))
c = cmp(BioGenerics.seqname(record), BioGenerics.groupname(interval))

if c < 0 || (c == 0 && BioGenerics.rightposition(record) < BioGenerics.leftposition(interval))
return -1
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8 changes: 4 additions & 4 deletions src/tabix.jl
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Expand Up @@ -70,16 +70,16 @@ end


"""
overlapchunks(tabix::Tabix, interval::Interval)
overlapchunks(tabix::Tabix, interval::GenomicInterval)

Return chunks possibly overlapping with the range specified by `interval`.

Note that records within the returned chunks are not guaranteed to actually overlap the query interval.
"""
function overlapchunks(tabix::Tabix, interval::Interval)
seqid = findfirst(isequal(BioGenerics.seqname(interval)), tabix.names)
function overlapchunks(tabix::Tabix, interval::GenomicInterval)
seqid = findfirst(isequal(BioGenerics.groupname(interval)), tabix.names)
if seqid == 0
throw(ArgumentError("failed to find sequence name '$(BioGenerics.seqname(interval))'"))
throw(ArgumentError("failed to find sequence name '$(BioGenerics.groupname(interval))'"))
end
return overlapchunks(tabix.index, seqid, BioGenerics.leftposition(interval):BioGenerics.rightposition(interval))
end
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