diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/c/multifasta_to_otu.c | 4 | ||||
| -rw-r--r-- | src/c/quikr.c | 1 |
2 files changed, 4 insertions, 1 deletions
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index e04ee12..8b26ee5 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -11,6 +11,10 @@ #include "nnls.h" #include "quikr_functions.h" +#ifdef Linux +#include <sys/sysinfo.h> +#endif + #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.\n\n-V, --version\n\tprint version." diff --git a/src/c/quikr.c b/src/c/quikr.c index c209515..a954cce 100644 --- a/src/c/quikr.c +++ b/src/c/quikr.c @@ -28,7 +28,6 @@ int main(int argc, char **argv) { long y = 0; int verbose = 0; - int debug = 0; int lambda = 10000; int kmer = 6; |