Implemented knucleotide in D (hanabi1224#355)

Code based on 8-m.rs and 1.zig codes with D analogues.

Author: cyrusmsk

bench/algorithm/knucleotide/1-m.d

@@ -0,0 +1,209 @@
+// port from 8-m.rs and 1.zig
+import std;
+import std.outbuffer : OutBuffer;
+
+alias Map = uint[Nullable!Code];
+static double hundreed = 100.0;
+
+static struct Code
+{
+ ulong data;
+
+ void push(ubyte c, ulong mask)
+ {
+ data = ((data << 2) | cast(ulong) c) & mask;
+ }
+
+ static Nullable!Code fromStr(ubyte[] s)
+ {
+ auto mask = Code.makeMask(s.length);
+ auto res = Code(0);
+ foreach (c; s)
+ res.push(Code.encodeByte(c), mask);
+ return nullable(res);
+ }
+
+ string toStr(size_t frame)
+ {
+ char[] res;
+ auto code = this.data;
+ ubyte c;
+ foreach (_; 0 .. frame)
+ {
+ switch (cast(ubyte) code & 0b11)
+ {
+ case Code.encodeByte('A'):
+ c = 'A';
+ break;
+ case Code.encodeByte('C'):
+ c = 'C';
+ break;
+ case Code.encodeByte('G'):
+ c = 'G';
+ break;
+ case Code.encodeByte('T'):
+ c = 'T';
+ break;
+ default:
+ break;
+ }
+ res ~= c;
+ code >>= 2;
+ }
+ return cast(string) res.reverse;
+ }
+
+ pragma(inline, true)
+ static ulong makeMask(size_t frame)
+ {
+ return (1L << (2 * frame)) - 1L;
+ }
+
+ pragma(inline, true)
+ static ubyte encodeByte(ubyte c)
+ {
+ return (c >> 1) & 0b11;
+ }
+}
+
+static struct CodeRange
+{
+ size_t i = 0;
+ ubyte[] input;
+ Nullable!Code code;
+ ulong mask;
+
+ bool empty() {
+ return this.i >= this.input.length;
+ }
+
+ Nullable!Code front() {
+ const c = this.input[this.i];
+ this.code.get.push(c, this.mask);
+ return this.code;
+ }
+
+ void popFront() {
+ this.i += 1;
+ }
+
+ this(ubyte[] input, size_t frame)
+ {
+ const mask = Code.makeMask(frame);
+ Nullable!Code tmpCode = Code(0);
+ foreach (c; input[0 .. frame - 1])
+ tmpCode.get.push(c, mask);
+ this.mask = mask;
+ this.code = tmpCode;
+ this.input = input[frame - 1 .. $];
+ }
+}
+
+Map genMap(Tuple!(ubyte[], size_t) t)
+{
+ Map myMap;
+ foreach(code; CodeRange(t[0], t[1]))
+ {
+ myMap.update(code,
+ () => 1,
+ (ref uint v) { v += 1; });
+ }
+ return myMap;
+}
+
+struct CountCode
+{
+ ulong count;
+ Nullable!Code code;
+}
+
+void printMap(size_t self, Map myMap, ref OutBuffer buf)
+{
+ CountCode[] v;
+ ulong total;
+ uint count;
+ foreach (pair; myMap.byPair)
+ {
+ total += pair.value;
+ v ~= CountCode(pair.value, pair.key);
+ }
+ alias asc = (a, b) =>
+ a.count < b.count ||
+ (a.count == b.count && b.code.get.data < a.code.get.data);
+
+ v.sort!(asc);
+
+ foreach (i; iota(cast(int)(v.length) - 1, -1, -1))
+ {
+ auto cc = v[i];
+ buf.writefln("%s %.3f", cc.code.get.toStr(self), cast(double) cc.count / cast(
+ double) total * hundreed);
+ }
+ buf.write("\n");
+}
+
+void printOcc(ubyte[] s, ref Map myMap, ref OutBuffer buf)
+{
+ auto tmp = Code.fromStr(s);
+ buf.writefln("%d\t%s", myMap.get(tmp, 0), cast(string) s);
+}
+
+ubyte[] readInput(string[] args)
+{
+ immutable fileName = args.length > 1 ? args[1] : "25000_in";
+ char key = '>';
+ ubyte[] res;
+ auto app = appender(&res);
+ app.reserve(65_536);
+ auto file = File(args[1]);
+ byte x = 3;
+ foreach (line; file.byLine())
+ {
+ if (line[0] == key)
+ x--;
+ else
+ continue;
+ if (x == 0)
+ break;
+ }
+ foreach (line; file.byChunk(61))
+ {
+ app ~= line[0..$-1].map!(a => Code.encodeByte(a));
+ }
+
+ return res;
+}
+
+void main(string[] args)
+{
+ auto buf1 = new OutBuffer();
+ auto buf2 = new OutBuffer();
+
+ static ubyte[][5] occs = [
+ cast(ubyte[]) "GGTATTTTAATTTATAGT",
+ cast(ubyte[]) "GGTATTTTAATT",
+ cast(ubyte[]) "GGTATT",
+ cast(ubyte[]) "GGTA",
+ cast(ubyte[]) "GGT",
+ ];
+ auto input = readInput(args);
+
+ alias myTaskType = Task!(run, uint[Nullable!(Code)]function(Tuple!(ubyte[], ulong)), Tuple!(ubyte[], ulong))*;
+ myTaskType[] calls;
+ foreach (i; 0 .. occs.length)
+ {
+ auto t = task(&genMap, tuple(input, occs[i].length));
+ t.executeInNewThread();
+ calls ~= t;
+ }
+
+ printMap(1, genMap(tuple(input, 1UL)), buf1);
+ printMap(2, genMap(tuple(input, 2UL)), buf1);
+
+ foreach (i; iota(4, -1, -1))
+ {
+ printOcc(occs[i], calls[i].yieldForce(), buf2);
+ }
+ write(buf1);
+ write(buf2);
+}

bench/bench_d.yaml

@@ -51,6 +51,9 @@ problems:
  - 1-im.d
  - 2-i.d
  - 2-im.d
+ - name: knucleotide
+ source:
+ - 1-m.d
 compiler_version_command:
 compiler_version_regex:
 runtime_version_parameter: