fast int to str

CHANGES.md

@@ -2,6 +2,7 @@
 =====
 + modifies region.dist.txt to contain the aggregate coverage of each window when -b (integer) is specified
   (otherwise region.dist.txt and global.disk.txt are identical with -b (integer) )
++ improve speed by ~30% when using per-base output with better int2str method
 
 0.2.8
 =====

int2str.nim

@@ -0,0 +1,95 @@
+import bitops
+
+#[
+
+this intToStr is adpated from: https://github.com/miloyip/itoa-benchmark countlut method.
+
+https://github.com/miloyip/itoa-benchmark/blob/master/license.txt
+Copyright (C) 2014 Milo Yip
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+]#
+
+
+const gDigitsLut = [
+    '0','0','0','1','0','2','0','3','0','4','0','5','0','6','0','7','0','8','0','9',
+    '1','0','1','1','1','2','1','3','1','4','1','5','1','6','1','7','1','8','1','9',
+    '2','0','2','1','2','2','2','3','2','4','2','5','2','6','2','7','2','8','2','9',
+    '3','0','3','1','3','2','3','3','3','4','3','5','3','6','3','7','3','8','3','9',
+    '4','0','4','1','4','2','4','3','4','4','4','5','4','6','4','7','4','8','4','9',
+    '5','0','5','1','5','2','5','3','5','4','5','5','5','6','5','7','5','8','5','9',
+    '6','0','6','1','6','2','6','3','6','4','6','5','6','6','6','7','6','8','6','9',
+    '7','0','7','1','7','2','7','3','7','4','7','5','7','6','7','7','7','8','7','9',
+    '8','0','8','1','8','2','8','3','8','4','8','5','8','6','8','7','8','8','8','9',
+    '9','0','9','1','9','2','9','3','9','4','9','5','9','6','9','7','9','8','9','9'
+];
+
+const powers_of_10 = [
+        0'i32,
+        10,
+        100,
+        1000,
+        10000,
+        100000,
+        1000000,
+        10000000,
+        100000000,
+        1000000000]
+
+proc countdigits(value:int32): int {.inline.} =
+  result = (32 - countLeadingZeroBits(value or 1)) * 1233 shr 12
+  result = result - int(value < powers_of_10[result]) + 1
+
+proc fastIntToStr*(value:int32, outstr:var string) {.inline.} =
+  outstr.setLen(countdigits(value))
+  var value = value
+  var L = outstr.high
+  while value >= 100:
+    let i = (value mod 100) shl 1
+    value = int32(value / 100)
+
+    outstr[L] = gDigitsLut[i + 1]
+    outstr[L-1] = gDigitsLut[i]
+    L -= 2
+  if value < 10:
+    outstr[L] = (value + '0'.int).char
+
+  else:
+    let i = value shl 1
+    outstr[L] = gDigitsLut[i + 1]
+    outstr[L-1] = gDigitsLut[i]
+
+
+when isMainModule:
+
+  import times
+  import strutils
+
+  var t0 = cpuTime()
+  var outstr = newString(10)
+  for i in 0'i32..200_000_000:
+    fastIntToStr(i, outstr)
+    #doAssert outstr == $i
+  echo cpuTime() - t0
+
+  t0 = cpuTime()
+  echo "only to 100m for $"
+  for i in 0'i32..100_000_000:
+    let outstr = intToStr(i)
+  echo cpuTime() - t0

mosdepth.nim

@@ -1,5 +1,6 @@
 import hts
 import tables
+import ./int2str
 import strutils as S
 import algorithm as alg
 import sequtils as sequtils
@@ -663,8 +664,19 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16
       if tid == -2:
         discard fbase.write_interval(starget & "0\t" & intToStr(int(target.length)) & "\t0", target.name, 0, int(target.length))
       else:
+        var line = newStringOfCap(32)
+        line.add(starget)
+        var start = newString(12)
+        var stop = newString(12)
+        var value = newString(8)
         for p in gen_depths(arr):
-          discard fbase.write_interval(starget & intToStr(p.start) & "\t" & intToStr(p.stop) & "\t" & intToStr(p.value), target.name, p.start, p.stop)
+          line.setLen(starget.len)
+          fastIntToStr(p.start.int32, start)
+          fastIntToStr(p.stop.int32, stop)
+          fastIntToStr(p.value.int32, value)
+          line.add(start); line.add('\t')
+          line.add(stop); line.add('\t'); line.add(value)
+          discard fbase.write_interval(line, target.name, p.start, p.stop)
     if quantize.len != 0:
       if tid == -2 and quantize[0] == 0:
         var lookup = make_lookup(quantize)