BGI/SOAPdenovo2/standardPregraph/inc/newhash.h

   1 /*
   2  * inc/newhash.h
   3  *
   4  * Copyright (c) 2008-2012 BGI-Shenzhen <soap at genomics dot org dot cn>.
   5  *
   6  * This file is part of SOAPdenovo.
   7  *
   8  * SOAPdenovo is free software: you can redistribute it and/or modify
   9  * it under the terms of the GNU General Public License as published by
  10  * the Free Software Foundation, either version 3 of the License, or
  11  * (at your option) any later version.
  12  *
  13  * SOAPdenovo is distributed in the hope that it will be useful,
  14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  16  * GNU General Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License
  19  * along with SOAPdenovo.  If not, see <http://www.gnu.org/licenses/>.
  20  *
  21  */
  22
  23 #ifndef __NEW_HASH_RJ
  24 #define __NEW_HASH_RJ
  25
  26 #ifndef K_LOAD_FACTOR
  27 #define K_LOAD_FACTOR 0.75
  28 #endif
  29
  30 #define MAX_KMER_COV 63
  31 #define EDGE_BIT_SIZE 6 //6 bit for each edge
  32 #define EDGE_XOR_MASK 0x3FU
  33 #define LINKS_BITS 0x00FFFFFFU
  34
  35 #define get_kmer_seq(mer) ((mer).seq)
  36 #define set_kmer_seq(mer, val) ((mer).seq = val)
  37
  38 #define get_kmer_left_cov(mer, idx) (((mer).l_links>>((idx)*EDGE_BIT_SIZE))&EDGE_XOR_MASK)
  39 #define set_kmer_left_cov(mer, idx, val) ((mer).l_links = ((mer).l_links&(~(EDGE_XOR_MASK<<((idx)*EDGE_BIT_SIZE)))) | (((val)&EDGE_XOR_MASK)<<((idx)*EDGE_BIT_SIZE)) )
  40 #define get_kmer_left_covs(mer) (get_kmer_left_cov(mer, 0) + get_kmer_left_cov(mer, 1) + get_kmer_left_cov(mer, 2) + get_kmer_left_cov(mer, 3))
  41
  42 #define get_kmer_right_cov(mer, idx) (((mer).r_links>>((idx)*EDGE_BIT_SIZE))&EDGE_XOR_MASK)
  43 #define set_kmer_right_cov(mer, idx, val) ((mer).r_links = ((mer).r_links&(~(EDGE_XOR_MASK<<((idx)*EDGE_BIT_SIZE)))) | (((val)&EDGE_XOR_MASK)<<((idx)*EDGE_BIT_SIZE)) )
  44 #define get_kmer_right_covs(mer) (get_kmer_right_cov(mer, 0) + get_kmer_right_cov(mer, 1) + get_kmer_right_cov(mer, 2) + get_kmer_right_cov(mer, 3))
  45
  46
  47 #define is_kmer_entity_null(flags, idx)    ((flags)[(idx)>>4]>>(((idx)&0x0f)<<1)&0x01)
  48 #define is_kmer_entity_del(flags, idx)     ((flags)[(idx)>>4]>>(((idx)&0x0f)<<1)&0x02)
  49 #define set_kmer_entity_null(flags, idx)   ((flags)[(idx)>>4] |= (0x01u<<(((idx)&0x0f)<<1)))
  50 #define set_kmer_entity_del(flags, idx)    ((flags)[(idx)>>4] |= (0x02u<<(((idx)&0x0f)<<1)))
  51 #define clear_kmer_entity_null(flags, idx) ((flags)[(idx)>>4] &= ~(0x01u<<(((idx)&0x0f)<<1)))
  52 #define clear_kmer_entity_del(flags, idx)  ((flags)[(idx)>>4] &= ~(0x02u<<(((idx)&0x0f)<<1)))
  53 #define exists_kmer_entity(flags, idx)     (!((flags)[(idx)>>4]>>(((idx)&0x0f)<<1)&0x03))
  54
  55 #ifdef MER127
  56 typedef __uint128_t u128b;
  57
  58 typedef struct u256b
  59 {
  60         u128b low;
  61         u128b high;
  62 } U256b;
  63 #else
  64 #endif
  65
  66 typedef struct kmer_st
  67 {
  68         Kmer seq;       //kmer set
  69         ubyte4 l_links;                     // sever as edgeID since make_edge
  70         ubyte4 r_links: 4 * EDGE_BIT_SIZE;
  71         ubyte4 linear: 1;
  72         ubyte4 deleted: 1;
  73         ubyte4 checked: 1;
  74         ubyte4 single: 1;
  75         ubyte4 twin: 2;
  76         ubyte4 inEdge: 2;
  77 } kmer_t;
  78
  79 typedef struct kmerSet_st
  80 {
  81         kmer_t * array; //kmer set
  82         ubyte4 * flags; //mark the element pos that exist in array
  83         ubyte8 size;
  84         ubyte8 count;
  85         ubyte8 max;
  86         float load_factor;
  87         ubyte8 iter_ptr;    //iter in set
  88 } KmerSet;
  89
  90 typedef struct kmer_pt
  91 {
  92         kmer_t * node;
  93         Kmer kmer;
  94         boolean isSmaller;
  95         struct kmer_pt * next;
  96 } KMER_PT;
  97
  98 extern KmerSet * init_kmerset ( ubyte8 init_size, float load_factor );
  99 extern int search_kmerset ( KmerSet * set, Kmer seq, kmer_t ** rs );
 100 extern int put_kmerset ( KmerSet * set, Kmer seq, ubyte left, ubyte right, kmer_t ** kmer_p );
 101 extern byte8 count_kmerset ( KmerSet * set );
 102 extern void free_Sets ( KmerSet ** KmerSets, int num );
 103 extern void free_kmerset ( KmerSet * set );
 104 extern void dislink2nextUncertain ( kmer_t * node, char ch, boolean smaller );
 105 extern void dislink2prevUncertain ( kmer_t * node, char ch, boolean smaller );
 106
 107 extern int count_branch2prev ( kmer_t * node );
 108 extern int count_branch2next ( kmer_t * node );
 109 extern char firstCharInKmer ( Kmer kmer );
 110
 111 #endif