tools/data_tools/filterReads.c

   1 ////////////////////////////////////////////////////////////
   2 // The purpose of this program is to read a gff and a
   3 // solexa reads file and create a data set used by QPalma.
   4 //
   5 //
   6 //
   7 //
   8 ////////////////////////////////////////////////////////////
   9
  10 #include <sys/mman.h>
  11 #include <stdio.h>
  12 #include <stdlib.h>
  13 #include <string.h>
  14
  15 #include "datastructures.h"
  16
  17 void parse_gff(char* filename,FILE* fid,struct gene* allGenes);
  18
  19 static char *info = "Usage is:\n./filterReads gff reads";
  20
  21 int main(int argc, char* argv[]) {
  22
  23    if(argc != 3) {
  24       printf("%s\n",info);
  25       exit(EXIT_FAILURE);
  26    }
  27
  28    //static size_t page_size;
  29    // page_size = (size_t) sysconf (_SC_PAGESIZE);
  30    int filenameSize = 256;
  31    char *gff_filename = malloc(sizeof(char)*filenameSize);
  32    char *reads_filename = malloc(sizeof(char)*filenameSize);
  33
  34    strncpy(gff_filename,argv[1],filenameSize);
  35    strncpy(reads_filename,argv[2],filenameSize);
  36
  37    FILE *gff_fs = fopen(gff_filename,"r");
  38    FILE *reads_fs = fopen(reads_filename,"r");
  39
  40    if(gff_fs == NULL) {
  41       printf("Error: Could not open file: %s",gff_filename);
  42       exit(EXIT_FAILURE);
  43    }
  44
  45    if(reads_fs == NULL) {
  46       printf("Error: Could not open file: %s",reads_filename);
  47       exit(EXIT_FAILURE);
  48    }
  49
  50    struct gene **allGenes;
  51    parse_gff(gff_filename,gff_fs,allGenes);
  52
  53
  54    int reads_fid = fileno(reads_fs);
  55    size_t mmapAreaSize = 16;
  56    void *reads_area = mmap (NULL,mmapAreaSize,PROT_READ|PROT_WRITE,MAP_PRIVATE,reads_fid,0);
  57    if((long int) reads_area == -1)
  58       printf("mmapping failed!\n");
  59
  60    char *test_string = malloc(sizeof(char)*10);
  61    strncpy(test_string,(char*)reads_area,10);
  62    //printf("Reads area at %s\n",test_string);
  63
  64    int status = munmap(reads_area,mmapAreaSize);
  65    if(status != 0)
  66       printf("munmap failed!\n");
  67
  68    status = fclose(gff_fs);
  69    status += fclose(reads_fs);
  70    if(status != 0)
  71       printf("closing of filestreams failed!\n");
  72
  73    printf("sizeof(struct gene) %d\n",sizeof(struct gene));
  74    printf("sizeof(struct read) %d\n",sizeof(struct read));
  75
  76
  77    free(gff_filename);
  78    free(reads_filename);
  79    return 0;
  80 }