This directory contains code to perform haplotype motif detection as
described in the paper "Haplotype Motifs: An Algorithmic Approach to
Locating Evolutionarily Conserved Patterns in Haploid Sequences" by
R. Schwartz, as well as various associated analysis steps to be
described in future publications.  Please refer to the paper for more
detailed information on the algorithms, the problems they solve, and
prior work in the area. This paper will appear in the Proceedings
of the Second IEEE Computer Society Bioinformatics Conference.

This directory should include the following files:
README.1st:		this file
README.hapmotif:	general documentation for hapmotif
README.htsnp:		general documentation for htsnp
README.predict:		general documentation for predictb and predictg
README.case-control:	general documentation for case-control
README.files:		guide to file formats used by the programs
haplotype-motif.cc:	primary source code for hapmotif
haplotype-motif.h:	header file for the source code for hapmotif
htsnp.cc:		primary source code for htsnp
htsnp.h:		header file for the source code for htsnp
predict-base.cc:	primary source code for predictb
predict-base.h:		header file for the source code for predictb
predict-global.cc:	primary source code for predictg
predict-global.h:	header file for the source code for predictg
case-control.cc:	primary source code for case-control
case-control.h:		header file for the source code for case-control
haplotype.h:		auxiliary Haplotype class
motif.h:		auxiliary Motif class
Makefile.linux:		Makefile for linux computers
Makefile.osx:		Makefile for Macintosh OS X computers
sample.hap:		a sample haplotype file

The code produces the following executables, whose operations are
described in the indicated README files:

hapmotif: README.hapmotif
htsnp: README.htsnp
predictb and predictg: README.predict
case-control: README.case-control

Default instructions for building the code on a Unix-based system
are as follows:

1. Choose the Makefile closer to your system.  If you are using Linux
or OS X and have Gnu g++ installed, one of the two files may work for
you directly.  For other Unix systems, Makefile.linux is probably the
more generic of the two.
2. Copy your chosen file into a new file named "Makefile".  For
example, if you are working with Makefile.linux, enter:
	cp Makefile.linux Makefile
3. Edit the Makefile so that CPP is the name of an ANSI C++ compiler
with whatever arguments you desire and INCLUDE and LIBS provide
whatever information the C++ compiler needs to find the include and
library directories needed for general compilation.  If you do not
have a C++ compiler, you will not be able to build the executables.
4. Type "make" to make the executables.

Following these instructions should produce the following executables:

hapmotif       code for finding conserved motifs in haploid sequences

htsnp          code for finding informative "haplotype tagging SNPs"
	       from a set of conserved motifs

predictb       two programs for predicting missing sites in haploid
  and          sequences or screening out likely recent mutations
predictg       using haplotype motifs

case-control   code for using haplotype motifs in case-control
               association testing

See the executable-specific README files for instructions on their
use.