2 files changed, 6 insertions, 1 deletions
diff --git a/src/c/multifasta_to_otu.1 b/src/c/multifasta_to_otu.1
index 748e9e9..d047ad1 100644
--- a/src/c/multifasta_to_otu.1
+++ b/src/c/multifasta_to_otu.1
@@ -5,6 +5,8 @@ multifasta_to_otu \- create a QIIME OTU table based on Quikr results.
 .B multifasta_to_otu
 .RB [ \-i
 .IR input-directory ]
+.RB [ \-f
+.IR input-filelist ]
 .RB [ \-s
 .IR sensing-matrix]
 .RB [ \-k
@@ -29,6 +31,9 @@ number of times a specimen was seen in all of the samples.
 .B \-i, --input-directory
 the directory containing the samples' fasta files of reads (note each fasta file should correspond to a separate sample)
 .TP
+.B \-f, --input-filelist
+a file containing list of fasta files to process seperated by newline (same rules apply as input-directory)
+.TP
 .B \-s, --sensing-matrix
 location of the sensing matrix.
 .TP
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c
index b6b0182..32cc3e9 100644
--- a/src/c/multifasta_to_otu.c
+++ b/src/c/multifasta_to_otu.c
@@ -20,7 +20,7 @@
 
 #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-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."
+#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, --input-filelist\n\ta file containing list of fasta files to process seperated by newline (same rules apply as input-directory)\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."
 
 static int cmp (const void * a, const void * b) {
 	return ( *(double*)a - *(double*)b );