remove all references to sensing-fasta

3 files changed, 3 insertions, 14 deletions

diff --git a/src/c/multifasta_to_otu.1 b/src/c/multifasta_to_otu.1
index 63e08b8..748e9e9 100644
--- a/src/c/multifasta_to_otu.1
+++ b/src/c/multifasta_to_otu.1
@@ -5,8 +5,6 @@ multifasta_to_otu \- create a QIIME OTU table based on Quikr results.
 .B multifasta_to_otu
 .RB [ \-i
 .IR input-directory ]
-.RB [ \-f
-.IR sensing-fasta]
 .RB [ \-s
 .IR sensing-matrix]
 .RB [ \-k
@@ -31,9 +29,6 @@ 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, --sensing-fasta
-location of the fasta file database used to create the sensing matrix.
-.TP
 .B \-s, --sensing-matrix
 location of the sensing matrix.
 .TP
diff --git a/src/c/quikr.1 b/src/c/quikr.1
index 89969a6..4418a7f 100644
--- a/src/c/quikr.1
+++ b/src/c/quikr.1
@@ -5,8 +5,6 @@ quikr \- Calculate estimated frequencies of bacteria in a sample.
 .B quikr
 .RB [ \-i
 .IR input]
-.RB [ \-f
-.IR sensing-fasta]
 .RB [ \-s
 .IR sensing-matrix]
 .RB [ \-l
@@ -29,9 +27,6 @@ input FASTA file and a trained sensing matrix
 .B \-i, --input
 the sample's fasta file of NGS. READS (fasta format)
 .TP
-.B \-f, --sensing-fasta
-location of the fasta file database used to create the sensing matrix. (fasta format)
-.TP
 .B \-s, --sensing-matrix
 location of the sensing matrix. (trained from quikr_train)
 .TP
@@ -52,7 +47,7 @@ print version.
 .SH EXAMPLES
 Use quikr to calculate the estimated frequencies for sample.fa, using rdp7.fasta as the sensing matrix we generated with quikr_train. This uses 6-mers by default, and a lambda value of 10000:
 .P
-quikr -i sample.fa -f rdp7.fa -s rdp_sensing_matrix.gz -o frequencies.txt
+quikr -i sample.fa -s rdp_sensing_matrix.gz -o frequencies.txt
 .SH "SEE ALSO"
 \fBmultifasta_to_otu\fP(1), \fBquikr_train\fP(1).
 .SH AUTHORS
diff --git a/src/c/quikr.c b/src/c/quikr.c
index af6275e..1465089 100644
--- a/src/c/quikr.c
+++ b/src/c/quikr.c
@@ -13,7 +13,7 @@
 #include "quikr.h"
 
 #define sensing_matrix(i,j) (sensing_matrix[width*i + j])
-#define USAGE "Usage:\n\tquikr [OPTION...] - Calculate estimated frequencies of bacteria in a sample.\n\nOptions:\n\n-i, --input\n\tthe sample's fasta file of NGS READS (fasta format)\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. (trained 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-o, --output\n\tOTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output)\n\n-v, --verbose\n\tverbose mode.\n\n-V, --version\n\tprint version."
+#define USAGE "Usage:\n\tquikr [OPTION...] - Calculate estimated frequencies of bacteria in a sample.\n\nOptions:\n\n-i, --input\n\tthe sample's fasta file of NGS READS (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (trained 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-o, --output\n\tOTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output)\n\n-v, --verbose\n\tverbose mode.\n\n-V, --version\n\tprint version."
 
 int main(int argc, char **argv) {
 
@@ -38,7 +38,6 @@ int main(int argc, char **argv) {
       {"kmer",  required_argument, 0, 'k'},
       {"lambda",  required_argument, 0, 'l'},
       {"output", required_argument, 0, 'o'},
-      {"sensing-fasta",  required_argument, 0, 'f'},
       {"sensing-matrix", required_argument, 0, 's'},
       {"verbose", no_argument, 0, 'v'},
       {"version", no_argument, 0, 'V'},
@@ -49,7 +48,7 @@ int main(int argc, char **argv) {
 
     int option_index = 0;
 
-    c = getopt_long (argc, argv, "k:l:f:s:i:o:hdvV", long_options, &option_index);
+    c = getopt_long (argc, argv, "k:l:s:i:o:hdvV", long_options, &option_index);
 
     if (c == -1)
       break;