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| author | Calvin Morrison <mutantturkey@gmail.com> | 2013-09-05 14:55:50 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2013-09-05 14:55:50 -0400 |
| commit | 2f62ad7c4ec7ed5bae74c4444442dd871222e6c6 (patch) | |
| tree | 453eea9193dbc5c3ca308f577c729d5f9f36d032 /src/c/multifasta_to_otu.c | |
| parent | 0d5cf0808f5ea0053526f485c40d5c67238b818c (diff) | |
last fixes for 1.0.4v1.0.4
Diffstat (limited to 'src/c/multifasta_to_otu.c')
| -rw-r--r-- | src/c/multifasta_to_otu.c | 4 |
1 files changed, 4 insertions, 0 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." |