BGI/SOAPdenovo2/sparsePregraph/inc/core.h

   1 /*
   2  * inc/core.h
   3  *
   4  * This file is part of SOAPdenovo.
   5  *
   6  * Part of this file is refered and modified from SparseAssembler
   7  * (See <http://sourceforge.net/projects/sparseassembler/>).
   8  *
   9  */
  10
  11 #ifndef _CORE_H
  12 #define _CORE_H
  13
  14 #include "stdinc.h"
  15
  16
  17 #ifdef _63MER_
  18 struct kmer_t2 //use union later
  19 {
  20         uint64_t kmer[2];
  21 };
  22 #endif
  23
  24
  25 #ifdef _127MER_
  26 struct kmer_t2 //use union later
  27 {
  28         uint64_t kmer[4];
  29 };
  30 #endif
  31
  32
  33
  34 struct edge_node   // kmer-edge  the connection between sparse-kmer
  35 {
  36         uint64_t edge: 50, edge_cov: 7, len: 6, used: 1;
  37         struct edge_node * nxt_edge;
  38 };
  39
  40
  41 //#pragma pack(4)    // do pack(4)  later
  42 struct kmer_info
  43 {
  44         //uint8_t used:1,split_left:1,split_right:1,removed:1,flip:1,marked:1,repeat:1;
  45
  46         uint64_t used: 1, linear: 1, deleted: 1, single: 1, inEdge: 2, twin: 2, cov1: 16; //added for soapdenovo
  47
  48         //uint16_t cov1:16;
  49
  50         //uint32_t edge_id;//added for soapdenovo
  51
  52         struct edge_node * left;
  53         struct edge_node * right;
  54
  55
  56
  57 };
  58 struct kmer_info_r1
  59 {
  60         uint16_t cov1: 16;
  61 };
  62
  63 struct bucket2      //sparse-kmer
  64 {
  65         struct kmer_t2 kmer_t2;
  66         struct kmer_info kmer_info;
  67         bucket2 * nxt_bucket;
  68 };
  69
  70 struct bucket2_r1  //sparse-kmer struct  for round1 ,
  71 {
  72         struct kmer_t2 kmer_t2;
  73         struct kmer_info_r1 kmer_info;
  74         bucket2_r1 * nxt_bucket;
  75 };
  76
  77 struct hashtable2
  78 {
  79         struct bucket2 ** store_pos;
  80         size_t ht_sz;
  81 };
  82
  83 struct read_t //reads bits struct ...
  84 {
  85         uint64_t read_bits[100];
  86         int readLen;
  87 };
  88
  89
  90
  91 //function for hashtable
  92 //void Init_HT2(struct hashtable2* ht,size_t ht_sz);
  93 //bool look_up_in_a_list2_r1(struct kmer_t2 *seq,struct bucket2_r1 *** ptr);
  94 //bool look_up_in_a_list2(struct kmer_t2 *seq,struct bucket2 *** ptr);
  95 //void free_hashtable(hashtable2 *ht);
  96
  97 inline void Init_HT2 ( struct hashtable2 * ht, size_t ht_sz )
  98 {
  99         ht->ht_sz = ht_sz;
 100         ht->store_pos = ( struct bucket2 ** ) calloc ( ht_sz, sizeof ( struct bucket2 * ) );
 101
 102         for ( size_t i = 0; i < ht_sz; ++i )
 103         {
 104                 ht->store_pos[i] = NULL;
 105         }
 106 }
 107
 108
 109 inline bool look_up_in_a_list2_r1 ( struct kmer_t2 * seq, struct bucket2_r1 ** * ptr )
 110 {
 111         while ( ( **ptr ) != NULL )
 112         {
 113                 if ( memcmp ( & ( ( **ptr )->kmer_t2.kmer ), & ( seq->kmer ), sizeof ( kmer_t2 ) ) == 0 )
 114                 {
 115                         break;
 116                 }
 117
 118                 ( *ptr ) = & ( ( **ptr )->nxt_bucket );
 119         }
 120
 121         return ( ( **ptr ) != NULL );
 122 }
 123
 124 inline bool look_up_in_a_list2 ( struct kmer_t2 * seq, struct bucket2 ** * ptr )
 125 {
 126         while ( ( **ptr ) != NULL )
 127         {
 128                 if ( memcmp ( & ( ( **ptr )->kmer_t2.kmer ), & ( seq->kmer ), sizeof ( kmer_t2 ) ) == 0 )
 129                 {
 130                         break;
 131                 }
 132
 133                 ( *ptr ) = & ( ( **ptr )->nxt_bucket );
 134         }
 135
 136         return ( ( **ptr ) != NULL );
 137 }
 138
 139 inline void free_bucket ( bucket2 * tmp )
 140 {
 141         edge_node * edge, *edge2;
 142         edge = tmp->kmer_info.left;
 143
 144         while ( edge )
 145         {
 146                 edge2 = edge;
 147                 edge = edge->nxt_edge;
 148                 free ( edge );
 149         }
 150
 151         edge = tmp->kmer_info.right;
 152
 153         while ( edge )
 154         {
 155                 edge2 = edge;
 156                 edge = edge->nxt_edge;
 157                 free ( edge );
 158         }
 159
 160         free ( tmp );
 161 }
 162 inline void free_hashtable ( hashtable2 * ht )
 163 {
 164         bucket2 * tmp, *tmp2;
 165
 166         for ( size_t i = 0; i < ht->ht_sz; ++i )
 167         {
 168                 tmp = ( ht->store_pos ) [i];
 169
 170                 while ( tmp )
 171                 {
 172                         tmp2 = tmp;
 173                         tmp = tmp->nxt_bucket;
 174                         free ( tmp2 );
 175                 }
 176         }
 177
 178         free ( ht->store_pos );
 179 }
 180
 181
 182
 183
 184 #endif