diff options
Diffstat (limited to 'src/c/multifasta_to_otu.c')
| -rw-r--r-- | src/c/multifasta_to_otu.c | 9 |
1 files changed, 7 insertions, 2 deletions
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index 01a4f0e..6d704dd 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -13,7 +13,7 @@ #define sensing_matrix(i,j) (sensing_matrix[width*i + j]) #define solutions(i,j) (solutions[sequences*i+ j]) -#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - create a QIIME OTU table based on Quikr results. \n\nOptions:\n\n-i, --input-directory\n\tthe directory containing the samples' fasta files of reads (note each file should correspond to a separate sample)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (sensing from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-j, --jobs\n\t specifies how many jobs to run at once. (default value is the number of CPUs)\n\n-o, --output\n\tthe OTU table, with NUM_READS_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or a sequence table if not OTU's)\n\n-v, --verbose\n\tverbose mode." +#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - create a QIIME OTU table based on Quikr results. \n\nOptions:\n\n-i, --input-directory\n\tthe directory containing the samples' fasta files of reads (note each file should correspond to a separate sample)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (sensing from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-j, --jobs\n\t specifies how many jobs to run at once. (default value is the number of CPUs)\n\n-o, --output\n\tthe OTU table, with NUM_READS_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or a sequence table if not OTU's)\n\n-v, --verbose\n\tverbose mode.\n\n-V, --version\n\tprint version." int main(int argc, char **argv) { @@ -58,11 +58,12 @@ int main(int argc, char **argv) { {"sensing-fasta", required_argument, 0, 'f'}, {"sensing-matrix", required_argument, 0, 's'}, {"verbose", no_argument, 0, 'v'}, + {"version", no_argument, 0, 'V'}, {0, 0, 0, 0} }; int option_index = 0; - c = getopt_long (argc, argv, "k:l:f:s:i:o:j:hv", long_options, &option_index); + c = getopt_long (argc, argv, "k:l:f:s:i:o:j:hvV", long_options, &option_index); if (c == -1) break; @@ -92,6 +93,10 @@ int main(int argc, char **argv) { case 'v': verbose = 1; break; + case 'V': + printf("%s\n", VERSION); + exit(EXIT_SUCCESS); + break; case 'h': puts(USAGE); exit(EXIT_SUCCESS); |