millironx/XAM.jl
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Code Issues Releases Packages Activity

Preallocate

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This commit is contained in:
Ciarán O'Mara 2020-02-02 21:29:20 +11:00
parent 789cccbaff
commit b0069d6f27
1 changed files with 6 additions and 6 deletions
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12
src/bam/reader.jl
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@ -87,7 +87,7 @@ function init_bam_reader(input::BGZFStreams.BGZFStream)
A = read(input, UInt8) A = read(input, UInt8)
M = read(input, UInt8) M = read(input, UInt8)
x = read(input, UInt8) x = read(input, UInt8)
if B != UInt8('B') || A != UInt8('A') || M != UInt8('M') || x != 0x01 if B != UInt8('B') || A != UInt8('A') || M != UInt8('M') || x != 0x01
error("input was not a valid BAM file") error("input was not a valid BAM file")
end end
@ -97,16 +97,16 @@ function init_bam_reader(input::BGZFStreams.BGZFStream)
samreader = SAM.Reader(IOBuffer(read(input, textlen))) samreader = SAM.Reader(IOBuffer(read(input, textlen)))
# reference sequences # reference sequences
refseqnames = String[]
refseqlens = Int[]
n_refs = read(input, Int32) n_refs = read(input, Int32)
for _ in 1:n_refs refseqnames = Vector{String}(undef, n_refs)
refseqlens = Vector{Int}(undef, n_refs)
@inbounds for i in 1:n_refs
namelen = read(input, Int32) namelen = read(input, Int32)
data = read(input, namelen) data = read(input, namelen)
seqname = unsafe_string(pointer(data)) seqname = unsafe_string(pointer(data))
seqlen = read(input, Int32) seqlen = read(input, Int32)
push!(refseqnames, seqname) refseqnames[i] = seqname
push!(refseqlens, seqlen) refseqlens[i] = seqlen
end end
voffset = isa(input.io, Base.AbstractPipe) ? voffset = isa(input.io, Base.AbstractPipe) ?