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Improve performance of fqcnt_jl1_klib.jl #7

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Merged
merged 4 commits into from
May 21, 2020
Merged

Improve performance of fqcnt_jl1_klib.jl #7

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7fd4ff8
make readbyte type stable
bicycle1885 May 21, 2020
f1b09c2
do not count string length twice
bicycle1885 May 21, 2020
2984dc8
use unsafe_string to make strings
bicycle1885 May 21, 2020
15d9864
use memchr to find delimiter
bicycle1885 May 21, 2020
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4 changes: 2 additions & 2 deletions fqcnt/fqcnt_jl1_klib.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ function main(args)
n, slen, qlen = 0, 0, 0
while (r = read(fx)) != nothing
n += 1
slen += length(r.seq)
qlen += length(r.qual)
slen += sizeof(r.seq)
qlen += sizeof(r.qual)
end
println(n, "\t", slen, "\t", qlen)
end
Expand Down
21 changes: 13 additions & 8 deletions lib/Klib.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ function destroy!(b::ByteBuffer)
return ret
end

tostring(b::ByteBuffer, n::Int) = String(unsafe_wrap(Vector{UInt8}, b.a, n))
tostring(b::ByteBuffer, n::Int) = unsafe_string(b.a, n)

#
# GzFile
Expand Down Expand Up @@ -202,7 +202,7 @@ function readbyte(r::Bufio{T}) where {T<:IO}
end
c = r.buf[r.start]
r.start += 1
return c
return c % Int
end

trimret(buf::ByteBuffer, n) = n > 0 && unsafe_load(buf.a, n) == 0x0d ? n - 1 : n # remove trailing '\r' if present
Expand Down Expand Up @@ -237,17 +237,13 @@ function readuntil!(r::Bufio{T}, delim::Int = -1, offset = 0, keep::Bool = false
end
x = r.len + 1
if delim == -1 # use '\n' as the delimitor
for i = r.start:r.len
@inbounds if r.buf[i] == 0x0a x = i; break end
end
x = finddelimiter(0x0a, r.buf, r.start, r.len)
elseif delim == -2 # use ' ', '\t' or '\n' as the delimitor
for i = r.start:r.len
@inbounds if r.buf[i] == 0x20 || r.buf[i] == 0x09 || r.buf[i] == 0x0a x = i; break end
end
else
for i = r.start:r.len
@inbounds if r.buf[i] == delim x = i; break end
end
x = finddelimiter(UInt8(delim), r.buf, r.start, r.len)
end
l = keep && x <= r.len ? x - r.start + 1 : x - r.start
reserve!(r.bb, UInt64(offset + n + l))
Expand All @@ -260,6 +256,15 @@ function readuntil!(r::Bufio{T}, delim::Int = -1, offset = 0, keep::Bool = false
return n == 0 && r.iseof ? -1 : n
end

function finddelimiter(delim, buf, start, len)
ptr = pointer(buf, start)
p = ccall(:memchr, Ptr{Cvoid}, (Ptr{Cvoid}, Cint, Csize_t), ptr, delim, len - start + 1)
if p == C_NULL
return len + 1
end
return Int(p - ptr + start)
end

"""
Base.readline(r::Bufio{T}) where T<:IO

Expand Down