diff --git a/main.c b/main.c index ae28936..35b5d89 100644 --- a/main.c +++ b/main.c @@ -657,14 +657,12 @@ void help() { fprintf(stderr, " -g: Specify a translation table to use (default"); fprintf(stderr, " 11).\n"); fprintf(stderr, " -h: Print help menu and exit.\n"); - fprintf(stderr, " -i: Specify input file (default reads from "); - fprintf(stderr, "stdin).\n"); - fprintf(stderr, " -m: Treat runs of n's as masked sequence and do"); - fprintf(stderr, " not build genes across \n"); - fprintf(stderr, " them.\n"); - fprintf(stderr, " -n: Bypass the Shine-Dalgarno trainer and force"); - fprintf(stderr, " the program to scan\n"); - fprintf(stderr, " for motifs.\n"); + fprintf(stderr, " -i: Specify FASTA/Genbank input file (default "); + fprintf(stderr, "reads from stdin).\n"); + fprintf(stderr, " -m: Treat runs of N as masked sequence; don't"); + fprintf(stderr, " build genes across them.\n"); + fprintf(stderr, " -n: Bypass Shine-Dalgarno trainer and force"); + fprintf(stderr, " a full motif scan.\n"); fprintf(stderr, " -o: Specify output file (default writes to "); fprintf(stderr, "stdout).\n"); fprintf(stderr, " -p: Select procedure (single or meta). Default"); diff --git a/sequence.c b/sequence.c index 463c940..583fdc1 100644 --- a/sequence.c +++ b/sequence.c @@ -58,7 +58,7 @@ int read_seq_training(FILE *fp, unsigned char *seq, unsigned char *useq, else if(hdr == 1 && (line[0] == '/' && line[1] == '/')) hdr = 0; else if(hdr == 1) { if(strstr(line, "Expand") != NULL && strstr(line, "gap") != NULL) { - sscanf(strstr(line, "gap")+4, "%d", &gapsize); + sscanf(strstr(line, "gap")+4, "%u", &gapsize); if(gapsize < 1 || gapsize > MAX_LINE) { fprintf(stderr, "Error: gap size in gbk file can't exceed line"); fprintf(stderr, " size.\n"); @@ -169,7 +169,7 @@ int next_seq_multi(FILE *fp, unsigned char *seq, unsigned char *useq, } else if(reading_seq == 1) { if(strstr(line, "Expand") != NULL && strstr(line, "gap") != NULL) { - sscanf(strstr(line, "gap")+4, "%d", &gapsize); + sscanf(strstr(line, "gap")+4, "%u", &gapsize); if(gapsize < 1 || gapsize > MAX_LINE) { fprintf(stderr, "Error: gap size in gbk file can't exceed line"); fprintf(stderr, " size.\n");