diff options
| -rw-r--r-- | README | 1 | ||||
| -rwxr-xr-x | count_nucleobases.c | 19 |
2 files changed, 13 insertions, 7 deletions
@@ -3,4 +3,3 @@ random fasta tools: count_nucleobases - counts nucleobases (A, C, G, T) in fasta files sequence_lengths - print out length of each sequences sequence_end_points - print out the end position of each sequence (continuous) - diff --git a/count_nucleobases.c b/count_nucleobases.c index 8c05a07..d4dca06 100755 --- a/count_nucleobases.c +++ b/count_nucleobases.c @@ -4,10 +4,10 @@ #include <unistd.h> #include <stdint.h> #include <stdbool.h> +#include <errno.h> int main() { - ssize_t len = 0; - + size_t len = 0; unsigned long long counts[256] = {0}; char buffer[4096]; @@ -15,10 +15,10 @@ int main() { len = fread(&buffer, 1, 1, stdin); - if(len != NULL) { + if(errno) { if(buffer[0] == '>') { header = true; - while((len = fread(&buffer, 1, 4096, stdin)) != NULL) { + while((len = fread(&buffer, 1, 4096, stdin)) != 0) { unsigned int i = 0; for(i = 0; i < len; i++) { if(buffer[i] == '>') { @@ -32,8 +32,15 @@ int main() { } } } - } else { fprintf(stderr, "this does not look like a fasta file\n"); } - } else { fprintf(stderr, "could not read file\n"); } + } + 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'], |