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1a3c986152
- Update to use GenomicFeatures v2. - BioAlignments v2. - BioSequences v2. - Indexes v0.1.
55 lines
1 KiB
Julia
55 lines
1 KiB
Julia
# BAI
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# ===
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#
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# Index for BAM files.
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# An index type for the BAM file format.
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struct BAI
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# BGZF file index
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index::Indexes.BGZFIndex
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# number of unmapped reads
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n_no_coors::Union{Nothing, Int}
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end
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"""
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BAI(filename::AbstractString)
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Load a BAI index from `filename`.
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"""
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function BAI(filename::AbstractString)
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return open(read_bai, filename)
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end
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"""
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BAI(input::IO)
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Load a BAI index from `input`.
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"""
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function BAI(input::IO)
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return read_bai(input)
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end
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# Read a BAI object from `input`.
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function read_bai(input::IO)
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# check magic bytes
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B = read(input, UInt8)
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A = read(input, UInt8)
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I = read(input, UInt8)
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x = read(input, UInt8)
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if B != UInt8('B') || A != UInt8('A') || I != UInt8('I') || x != 0x01
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error("input is not a valid BAI file")
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end
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# read contents
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n_refs = read(input, Int32)
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index = Indexes.read_bgzfindex(input, n_refs)
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if !eof(input)
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n_no_coors = read(input, UInt64)
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else
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n_no_coors = nothing
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end
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return BAI(index, n_no_coors)
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end
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