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// Licensed to the .NET Foundation under one or more agreements.
// The .NET Foundation licenses this file to you under the MIT license.
// See the LICENSE file in the project root for more information.
// Adapted from reverse-complement C# .NET Core program
// http://benchmarksgame.alioth.debian.org/u64q/program.php?test=revcomp&lang=csharpcore&id=1
// aka (as of 2017-09-01) rev 1.2 of https://alioth.debian.org/scm/viewvc.php/benchmarksgame/bench/revcomp/revcomp.csharp?root=benchmarksgame&view=log
// Best-scoring single-threaded C# .NET Core version as of 2017-09-01
/* The Computer Language Benchmarks Game
http://benchmarksgame.alioth.debian.org/
contributed by Robert F. Tobler to process large blocks of byte arrays
*/
using System;
using System.IO;
using System.Collections.Generic;
using System.Security.Cryptography;
using Microsoft.Xunit.Performance;
using Xunit;
[assembly: OptimizeForBenchmarks]
namespace BenchmarksGame
{
public static class ReverseComplement_1
{
struct Block
{
public byte[] Data; public int Count;
public int Read(BinaryReader r)
{
Data = r.ReadBytes(16384); Count++; return Data.Length;
}
public Index IndexOf(byte b, int o)
{
return new Index { Block = Count, Pos = Array.IndexOf(Data, b, o) };
}
}
struct Index
{
public int Block; public int Pos;
public static readonly Index None = new Index { Block = -1, Pos = -1 };
public bool InBlock(Block b) { return Block == b.Count; }
}
const byte Gt = (byte)'>';
const byte Lf = (byte)'\n';
static int Main(string[] args)
{
var helpers = new TestHarnessHelpers(bigInput: false);
var outBytes = new byte[helpers.FileLength];
using (var input = new FileStream(helpers.InputFile, FileMode.Open))
using (var output = new MemoryStream(outBytes))
{
Bench(input, output);
}
Console.WriteLine(System.Text.Encoding.UTF8.GetString(outBytes));
if (!MatchesChecksum(outBytes, helpers.CheckSum))
{
return -1;
}
return 100;
}
[Benchmark(InnerIterationCount = 1500)]
public static void RunBench()
{
var helpers = new TestHarnessHelpers(bigInput: true);
var outBytes = new byte[helpers.FileLength];
Benchmark.Iterate(() =>
{
using (var input = new FileStream(helpers.InputFile, FileMode.Open))
using (var output = new MemoryStream(outBytes))
{
Bench(input, output);
}
});
Assert.True(MatchesChecksum(outBytes, helpers.CheckSum));
}
static bool MatchesChecksum(byte[] bytes, string checksum)
{
using (var md5 = MD5.Create())
{
byte[] hash = md5.ComputeHash(bytes);
return (checksum == BitConverter.ToString(hash));
}
}
static void Bench(Stream input, Stream output)
{
InitComplements();
var seq = new List<byte[]>();
var b = new Block { Count = -1 };
Index line = Index.None, start = Index.None, end = Index.None;
using (var r = new BinaryReader(input))
{
using (var w = output)
{
while (b.Read(r) > 0)
{
seq.Add(b.Data);
if (line.Pos < 0) line = b.IndexOf(Gt, 0);
while (line.Pos >= 0)
{
if (start.Pos < 0)
{
var off = line.InBlock(b) ? line.Pos : 0;
start = b.IndexOf(Lf, off);
if (start.Pos < 0)
{
w.Write(b.Data, off, b.Data.Length - off);
seq.Clear(); break;
}
w.Write(b.Data, off, start.Pos + 1 - off);
}
if (end.Pos < 0)
{
end = b.IndexOf(Gt, start.InBlock(b) ? start.Pos : 0);
if (end.Pos < 0) break;
}
w.Reverse(start.Pos, end.Pos, seq);
if (seq.Count > 1) seq.RemoveRange(0, seq.Count - 1);
line = end; end = Index.None; start = Index.None;
}
}
if (start.Pos >= 0 && end.Pos < 0)
w.Reverse(start.Pos, seq[seq.Count - 1].Length, seq);
}
}
}
const string Seq = "ABCDGHKMRTVYabcdghkmrtvy";
const string Rev = "TVGHCDMKYABRTVGHCDMKYABR";
static byte[] comp = new byte[256];
static void InitComplements()
{
for (byte i = 0; i < 255; i++) comp[i] = i;
for (int i = 0; i < Seq.Length; i++)
comp[(byte)Seq[i]] = (byte)Rev[i];
comp[Lf] = 0; comp[(byte)' '] = 0;
}
const int LineLen = 61;
const int BufSize = LineLen * 269;
static byte[] buf = new byte[BufSize];
static void Reverse(this Stream w, int si, int ei, List<byte[]> bl)
{
int bi = 0, line = LineLen - 1;
for (int ri = bl.Count - 1; ri >= 0; ri--)
{
var b = bl[ri]; int off = ri == 0 ? si : 0;
for (int i = (ri == bl.Count - 1 ? ei : b.Length) - 1; i >= off; i--)
{
var c = comp[b[i]]; if (c > 0) buf[bi++] = c;
if (bi == line)
{
buf[bi++] = Lf; line += LineLen;
if (bi == BufSize)
{
w.Write(buf, 0, BufSize); bi = 0; line = LineLen - 1;
}
}
}
}
if (bi > 0)
{
if (buf[bi - 1] != Lf) buf[bi++] = Lf; w.Write(buf, 0, bi);
}
}
}
}
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