BGI/SOAPdenovo2/sparsePregraph/global.cpp

   1 /*
   2  * global.cpp
   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 #include "global.h"
  24
  25 char shortrdsfile[256];//in lib file
  26 char graphfile[256];//out prefix
  27
  28 int NodeCovTh = 1;
  29 int EdgeCovTh = 1; //BE :build edge ,BPA:build preArc
  30
  31 int K_size = 23;
  32 int gap = 15;
  33 uint64_t GenomeSize = 0;
  34 int solve = 0; //default not solving repeats
  35 int run_mode = 0;
  36
  37 int thrd_num_s = 8;
  38
  39 size_t * edge_cnt_total = NULL; //used int lock strategy
  40 size_t * bucket_count_total = NULL; //used in lock strategy
  41
  42
  43 //for io thread @see io_func.h
  44 //for io thread
  45 string * seq_t = NULL;
  46 int io_ready;       //0 ready to work 1 working 2 *seq_t ready 3 end reading signal
  47 int read_num = 0;   //the read num in *seq_t
  48
  49 string * read_buf0 = NULL;
  50 string * read_buf1 = NULL;
  51 int io_stat0 = 1; //must be one, if io_stat0 =0 ,the io thread will work immediately
  52 int io_stat1 = 1;
  53
  54 size_t reads_all_num = 0;
  55
  56 int max_rd_len = 0;
  57 int min_rd_len = 100000;
  58
  59
  60 //for the hashing lock strategy ...
  61 pthread_spinlock_t * locks;
  62
  63
  64
  65 // solving tiny repeats, temporarily using global vars to implements this feature
  66 unsigned int * mark_on_edge = NULL;
  67 pthread_spinlock_t * s_locks = NULL;
  68 struct edge_path_buffer ** path_buffer = NULL;
  69 unsigned long long buff_size = 1024;
  70 unsigned int max_path_length = 128; //max_path_length-1 is the real max path length, because the first int of buffer record the path length
  71
  72 FILE * mark_fp = NULL; //
  73 FILE * path_fp = NULL; //
  74 pthread_mutex_t file_lock;//
  75
  76 int debug = 0 ;
  77
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