Finish multiple thread counting

2026-10-11 01:10:56 +08:00 · 2019-05-12 02:16:20 -04:00
parent 94bd75e576
commit 9302fc6058
25 changed files with 1209 additions and 34 deletions
@@ -0,0 +1,89 @@
+#ifndef __KMER__
+#define __KMER__
+#include "Process_Read.h"
+
+#define ALL (0xffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff)
+
+#define SAFE_SHIFT(k) k & ((k < 64)?ALL:0)
+
+
+static unsigned char seq_nt6_table[256] = {
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 0, 5, 1,  5, 5, 5, 2,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  3, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 0, 5, 1,  5, 5, 5, 2,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  3, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
+    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5
+};
+
+
+
+typedef struct
+{
+    ///最大64-mer
+    ///x[0]低位
+    ///x[1]高位
+    uint64_t x[2];
+
+} Hash_code;
+
+
+
+typedef struct
+{
+	char* str;
+	long long l;
+    long long i;
+
+} HPC_seq;
+
+
+inline uint64_t get_HPC_code(HPC_seq* seq)
+{
+
+    if(seq->i < seq ->l)
+    {
+        char code = seq->str[seq->i];
+
+        for (; seq->i < seq->l; seq->i++)
+        {
+            if (seq->str[seq->i] != code)
+            {
+                break;
+            }
+        }
+
+        return (uint64_t)seq_nt6_table[(uint8_t)code];
+    }
+    else
+    {
+        ///end
+        return 6;
+    }
+    
+}
+
+inline void k_mer_append(Hash_code* code, uint64_t c, int k)
+{
+
+    uint64_t mask = ALL >> (64 -k);
+
+    code->x[0] = ((code->x[0]<<1) | (c&1))  & mask;
+    code->x[1] = ((code->x[1]<<1) | (c>>1)) & mask;
+}
+
+void init_HPC_seq(HPC_seq* seq, char* str, long long l);
+void init_Hash_code(Hash_code* code);
+
+
+#endif