BGI/SOAPdenovo2/standardPregraph/output_pregraph.c

   1 /*
   2  * 31mer/output_pregraph.c
   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 <stdinc.h>
  24 #include "newhash.h"
  25 #include "kmerhash.h"
  26 #include <extfunc.h>
  27 #include <extvab.h>
  28 static int outvCounter = 0;
  29
  30 //after this LINKFLAGFILTER in the Kmer is destroyed
  31 static void output1vt ( kmer_t * node1, FILE * fp )
  32 {
  33         if ( !node1 )
  34         {
  35                 return;
  36         }
  37
  38         if ( ! ( node1->linear ) && ! ( node1->deleted ) )
  39         {
  40                 outvCounter++;
  41                 print_kmer ( fp, node1->seq, ' ' );
  42
  43                 if ( outvCounter % 8 == 0 )
  44                 {
  45                         fprintf ( fp, "\n" );
  46                 }
  47         }
  48 }
  49
  50 void output_vertex ( char * outfile )
  51 {
  52         char temp[256];
  53         FILE * fp;
  54         int i;
  55         kmer_t * node;
  56         KmerSet * set;
  57         sprintf ( temp, "%s.vertex", outfile );
  58         fp = ckopen ( temp, "w" );
  59
  60         for ( i = 0; i < thrd_num; i++ )
  61         {
  62                 set = KmerSets[i];
  63                 set->iter_ptr = 0;
  64
  65                 while ( set->iter_ptr < set->size )
  66                 {
  67                         if ( !is_kmer_entity_null ( set->flags, set->iter_ptr ) )
  68                         {
  69                                 node = set->array + set->iter_ptr;
  70                                 output1vt ( node, fp );
  71                         }
  72
  73                         set->iter_ptr++;
  74                 }
  75         }
  76
  77         fprintf ( fp, "\n" );
  78         fprintf ( stderr, "%d vertex(es) output.\n", outvCounter );
  79         fclose ( fp );
  80         sprintf ( temp, "%s.preGraphBasic", outfile );
  81         fp = ckopen ( temp, "w" );
  82         fprintf ( fp, "VERTEX %d K %d\n", outvCounter, overlaplen );
  83         fprintf ( fp, "\nEDGEs %d\n", num_ed );
  84         fprintf ( fp, "\nMaxReadLen %d MinReadLen %d MaxNameLen %d\n", maxReadLen4all, minReadLen, maxNameLen );
  85         fclose ( fp );
  86 }
  87
  88 void output_1edge ( preEDGE * edge, gzFile * fp )
  89 {
  90         int i;
  91         gzprintf ( fp, ">length %d,", edge->length );
  92         print_kmer_gz ( fp, edge->from_node, ',' );
  93         print_kmer_gz ( fp, edge->to_node, ',' );
  94         gzprintf ( fp, "cvg %d, %d\n", edge->cvg, edge->bal_edge );
  95
  96         for ( i = 0; i < edge->length; i++ )
  97         {
  98                 gzprintf ( fp, "%c", int2base ( ( int ) edge->seq[i] ) );
  99
 100                 if ( ( i + 1 ) % 100 == 0 )
 101                 {
 102                         gzprintf ( fp, "\n" );
 103                 }
 104         }
 105
 106         if ( edge->length % 100 != 0 )
 107         {
 108                 gzprintf ( fp, "\n" );
 109         }
 110 }
 111
 112