From 0773aaf89678b967588a902df1f5e6f9ccea393d Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Tue, 14 May 2013 21:51:40 -0400
Subject: release1.0

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 create mode 100644 src/c/quikr.1

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diff --git a/src/c/quikr.1 b/src/c/quikr.1
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+.TH quikr 1 quikr-2013-05
+.SH NAME
+quikr \- Calculate estimated frequencies of bacteria in a sample.
+.SH SYNOPSIS
+.B quikr
+.RB [ \-i
+.IR input]
+.RB [ \-f
+.IR sensing-fasta]
+.RB [ \-s
+.IR sensing-matrix]
+.RB [ \-l
+.IR lambda ]
+.RB [ \-k
+.IR kmer ]
+.RB [ \-o
+.IR output ]
+.RB [ \-v ]
+.P
+.BR quikr " ..."
+.SH DESCRIPTION
+.B quikr
+Quikr returns the estimated frequencies of batcteria present when given a
+input FASTA file and a trained sensing matrix
+.P
+.SH OPTIONS
+.TP
+.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
+.B \-k, --kmer
+specify what size of kmer to use. (default value is 6)
+.TP
+.B \-l, --lambda
+lambda value to use. (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
+.B \-v, --verbose
+verbose mode.
+.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
+.SH "SEE ALSO"
+\fBmultifasta_to_otu\fP(1), \fBquikr_train\fP(1).
+.SH AUTHORS
+.B quikr
+was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison 
+<mutantturkey@gmail.com>, David Koslicki, Simon Foucart, Jean-Luc Bouchot
+.SH REPORTING BUGS
+.TP
+Please report all bugs to Gail Rosen <gailr@ece.drexel.edu>. Include your \
+operating system, current compiler, and test files to reproduce your issue.
+.SH COPYRIGHT.
+Copyright \(co 2013 by Calvin Morrison and Gail Rosen.  Permission to use, 
+copy, modify, distribute, and sell this software and its documentation for
+any purpose is hereby granted without fee, provided that the above copyright 
+notice appear in all copies and that both that copyright notice and this 
+permission noticeappear in supporting documentation.  No representations are
+made about the suitability of this software for any purpose.  It is provided
+"as is" without express or implied warranty.
+
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