update documentation

10 files changed, 12 insertions, 11 deletions

diff --git a/doc/.cli.markdown.swo b/doc/.cli.markdown.swo
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diff --git a/doc/.cli.markdown.swp b/doc/.cli.markdown.swp
new file mode 100644
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diff --git a/doc/.install.markdown.swo b/doc/.install.markdown.swo
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diff --git a/doc/.install.markdown.swp b/doc/.install.markdown.swp
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diff --git a/doc/.matlab.markdown.swp b/doc/.matlab.markdown.swp
new file mode 100644
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diff --git a/doc/install.markdown b/doc/install.markdown
index eb0e8ce..3308f83 100644
--- a/doc/install.markdown
+++ b/doc/install.markdown
@@ -5,23 +5,24 @@ To use Quikr there are several prerequisites.
 + Mac OS X 10.6.8 or GNU/Linux
 + 4Gb of RAM minimum. Absolutely neccessary.
 + gcc that supports OpenMP
-+ mlton the Standard-ML compiler
 
 ### Python Requirements ###
+*the python version is out of date*
 + Python 2.7+ 
 + Scipy 
 + Numpy
 + BioPython
 
+### Matlab Requrements ###
++ [dna\_utils](http://github.com/EESI/dna-utils/) must be installed
+
 ### Mac Requirements ###
 + Mac OS X 10.6.8 (what we have tested)
 + GCC 4.7 or newer. (gcc 4.2 did not work, and is the default installation)
-+ mlton the Standard-ML compiler
 + OpenMP libraries (libgomp, usually comes with gcc)
 
 ### Linux Requirements ###
 + GCC 4.7 or newer
-+ OCaml compiler mlton
 + OpenMP libraries (libgomp, usually comes with gcc)
 
 We also have a Quikr implementation in Matlab so that you can easily integrate
diff --git a/doc/matlab.markdown b/doc/matlab.markdown
index 09b0103..87a3a4d 100644
--- a/doc/matlab.markdown
+++ b/doc/matlab.markdown
@@ -2,13 +2,6 @@
 The Quikr implementation works in Matlab and also works in Octave, but the
 Octave version will run much slower.
 
-You will need to install the generate_kmers tool into your $PATH (eg /usr/bin/)
-this file is available in the src/python/ directory. If you use make to install
-the quikr project, it will already be installed. To test this you can run:
-
-    which generate_kmers
-    
-
 ## Quikr Example ##
 This is an example of how to run Quikr. Before you try the example please make
 make sure that you are in the quikr's matlab directory (src/matlab/):
diff --git a/doc/python.markdown b/doc/python.markdown
index df086d8..cbc59d1 100644
--- a/doc/python.markdown
+++ b/doc/python.markdown
@@ -1,3 +1,5 @@
+*The python version is outdated. do not use! It is only here for historical purposes!*
+
 # Python Documentation #
 The python version comes with scripts that can be used like the regular quikr
 program, and also a module called quikr so integration with python scripts 
@@ -12,6 +14,7 @@ If you want to use our quikr module, run help on the module:
 
     >>> import quikr
     >>> help(quikr)
+
 ## Python Cannot Find XYZ ##
 
 Ensure that you have Python 2.7, Scipy, Numpy, and BIOpython installed 
diff --git a/src/c/quikr.1 b/src/c/quikr.1
index 4418a7f..7d0baf6 100644
--- a/src/c/quikr.1
+++ b/src/c/quikr.1
@@ -36,6 +36,9 @@ specify what size of kmer to use. (default value is 6)
 .B \-l, --lambda
 lambda value to use. (default value is 10000)
 .TP
+.B \-r, --rare-percent
+remove mers from classification if their values are less than the x percentile of values in the sample (default value is 10000)
+.TP
 .B \-o, --output
 OTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output)
 .TP
@@ -52,7 +55,7 @@ quikr -i sample.fa -s rdp_sensing_matrix.gz -o frequencies.txt
 \fBmultifasta_to_otu\fP(1), \fBquikr_train\fP(1).
 .SH AUTHORS
 .B quikr
-was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison 
+was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison
 <mutantturkey@gmail.com>, David Koslicki, Simon Foucart, and Jean-Luc Bouchot.
 .SH REPORTING BUGS
 .TP
diff --git a/src/c/quikr.c b/src/c/quikr.c
index 01c5f63..de1f39a 100644
--- a/src/c/quikr.c
+++ b/src/c/quikr.c
@@ -115,6 +115,7 @@ int main(int argc, char **argv) {
 
 	if(verbose) {
 		printf("kmer: %u\n", kmer);
+		printf("rare: %lf\n", rare_percent);
 		printf("lambda: %llu\n", lambda);
 		printf("fasta: %s\n", input_fasta_filename);
 		printf("sensing matrix: %s\n", sensing_matrix_filename);