attempted to optimize, but little effect

lh3 · May 11, 2020 · db4ad26 · db4ad26
1 parent 54ece74
commit db4ad26
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@
 |:-------|:---------|:--------|--------------------:|---------------------:|--------------------:|---------------------:|
 |[bedcov\_c1\_cgr.c](bedcov/bedcov_c1_cgr.c)          |C         |[cgranges.h](lib/cgranges.h)|  5.5|  138.4 | 10.7|  19.1 |
 |[bedcov\_nim1\_klib.nim](bedcov/bedcov_nim1_klib.nim)|Nim       |[klib.nim](lib/klib.nim)    | 16.9|  497.7 | 25.7|  69.1 |
-|[bedcov\_jl1\_klib.jl](bedcov/bedcov_jl1_klib.jl)    |Julia     |[Klib.jl](lib/Klib.jl)      | 48.7| 6769.9 | 77.1| 290.4 |
+|[bedcov\_jl1\_klib.jl](bedcov/bedcov_jl1_klib.jl)    |Julia     |[Klib.jl](lib/Klib.jl)      | 45.2| 3657.7 | 77.4| 288.8 |
 |[bedcov\_js1\_k8.js](bedcov/bedcov_js1_k8.jl)        |Javascript|                            | 75.4| 2219.9 | 87.2| 316.8 |
 |[bedcov\_lua1.lua](bedcov/bedcov_lua1.lua)           |LuaJIT    |                            |174.1| 2668.0 |217.6| 364.6 |
 

diff --git a/bedcov/bedcov_jl1_klib.jl b/bedcov/bedcov_jl1_klib.jl
@@ -19,14 +19,15 @@ function main(args)
 	for ctg in keys(bed)
 		Klib.it_index!(bed[ctg])
 	end
+	b = Vector{Klib.Interval{Int}}()
 	for line in eachline(args[2])
 		t = split(line, "\t")
 		if get(bed, t[1], nothing) == nothing
 			println(t[1], "\t", t[2], "\t", t[3], "\t", 0, "\t", 0)
 		else
 			a = bed[t[1]]
 			st0, en0 = parse(Int, t[2]), parse(Int, t[3])
-			b = Klib.it_overlap(a, st0, en0)
+			Klib.it_overlap!(a, st0, en0, b)
 			cov_st, cov_en, cov = 0, 0, 0
 			for i = 1:length(b)
 				st1 = max(b[i].st, st0)

diff --git a/lib/Klib.jl b/lib/Klib.jl
@@ -1,7 +1,7 @@
 module Klib
 
 export getopt, GzFile, close, Bufio, readbyte, readuntil!, FastxReader, FastxRecord
-export Interval, it_index, it_overlap
+export Interval, it_index, it_overlap!
 
 #
 # Getopt iterator
@@ -383,9 +383,10 @@ function it_index!(a::Vector{Interval{T}}) where T<:Number
 	end
 end
 
-function it_overlap(a::Vector{Interval{T}}, st::Int, en::Int) where T<:Number
-	b = Vector{Interval{T}}()
+function it_overlap!(a::Vector{Interval{T}}, st::Int, en::Int, b::Vector{Interval{T}}) where T<:Number
+	resize!(b, 0)
 	stack = Vector{Tuple{Int,Int,Int}}()
+	sizehint!(stack, 128)
 	h = 0
 	while (1<<h <= length(a)) h += 1 end
 	h -= 1
@@ -412,7 +413,6 @@ function it_overlap(a::Vector{Interval{T}}, st::Int, en::Int) where T<:Number
 			push!(stack, (x + (1<<(h-1)), h - 1, 0))
 		end
 	end
-	return b
 end
 
 end # module Klib