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path: root/count_nucleobases.c
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// Copyright 2013 Calvin Morrison
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <stdint.h>
#include <stdbool.h>
#include <errno.h>
int main() {

  size_t len = 0;
	unsigned long long counts[256] = {0};

	char buffer[4096];
	bool header = false;

	len = fread(&buffer, 1, 1, stdin);

	if(errno) {
		if(buffer[0] == '>') {
			header = true;
			while((len = fread(&buffer, 1, 4096, stdin)) != 0) {
				unsigned int i = 0;
				for(i = 0; i < len; i++) {
					if(buffer[i] == '>') {
						header = true;
						continue;
					}
					else if(buffer[i] == '\n' && header == true) 
						header = false;
					if(header == false ) {
						counts[(int)buffer[i]]++;
					}
				}
			}
		}  
		else { 
			fprintf(stderr, "this does not look like a fasta file\n"); 
			exit(EXIT_FAILURE);
		}
	} else { 
		fprintf(stderr, "could not read file\n"); 
		exit(EXIT_FAILURE);
	}

	printf("A:%llu\nC:%llu\nG:%llu\nT:%llu\n",
         counts['a'] + counts['A'],
         counts['c'] + counts['C'],
         counts['g'] + counts['G'],
         counts['t'] + counts['T']);

 	return EXIT_SUCCESS;
}