88 lines
1.6 KiB
C
Executable File
88 lines
1.6 KiB
C
Executable File
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#include <stdio.h>
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#include <stdlib.h>
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#include <sys/mman.h> /* mmap() is defined in this header */
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#include <stdint.h>
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#include <fcntl.h>
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#include <sys/stat.h>
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#include "../obitypes.h"
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#include "../obidmscolumn.h"
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/**
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* @brief Computes the size to map.
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*
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* * @param OBIDMSColumn_file The file to map.
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* @return The size to map.
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*/
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int get_size_to_map(int OBIDMSColumn_file)
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// compute size to map : file size minus size of the header
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{
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int size;
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struct stat s;
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fstat(OBIDMSColumn_file, &s);
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size = (s.st_size) - HEADER_SIZE;
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return(size);
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}
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/**
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* @brief Computes and prints the total number of sequences by summing their counts.
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*
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* * @param The count file.
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*/
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int main(int argc, char const *argv[])
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{
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char* map;
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int size;
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int OBIDMSColumn_file;
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int count;
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char c;
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char num_str[10] = "";
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int num_int;
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int i,j;
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// initialize variables
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OBIDMSColumn_file = open(argv[1], O_RDONLY); //read only
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count = 0;
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j = 0;
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// compute size to map
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size = get_size_to_map(OBIDMSColumn_file);
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// map the data
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map = obi_map_read_only(OBIDMSColumn_file, HEADER_SIZE, size);
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// sum the counts
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for (i=0; i<size; i++)
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{
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c = map[i];
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if (c != SEPARATOR) // reading lines
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{
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num_str[j] = c;
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j++;
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}
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else if (c == SEPARATOR) // end of a line
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{
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num_int = atoi(num_str); // turn number from character string to int
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count = count + num_int; // add the number to the sum
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j = 0;
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num_str[j] = '\0';
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}
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}
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// print the final count of sequences
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fprintf(stderr, "Sequence count = %d\n", count);
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// unmap
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obi_unmap(size);
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// close file
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close(OBIDMSColumn_file);
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return(0);
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}
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