
// #######################################################################

// SSAHA : Sequence Search and Alignment by Hashing Algorithm
// Version 3.2, released 1st March 2004
// Copyright (c) Genome Research 2002

// SSAHA is free software; you can redistribute it and/or modify 
// it under the terms of version 2 of the GNU General Public Licence
// as published by the Free Software Foundation.
 
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public Licence for more details.
 
// There should be a copy of the GNU General Public Licence in the same
// directory as this file; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
// or see the on-line version at http://www.gnu.org/copyleft/gpl.txt

// #######################################################################

README file for SSAHA/Binary

The main ssaha executable and its associated library and test harnesses
are built in this directory.

This software was developed using version 2.95.2 of the GNU g++ compiler
on a Compaq Alpha. Earlier versions were also tested using the same compiler
and version on Linux, Sun and SGI machines. This version also compiles
and runs using g++ 3.0.3 on a Compaq Alpha, but this compiler version has
not been tested on other platforms.

Patched for linux/g++3.2.2 25/8/4 AWS.

This version was patched for Linux/GCC 4.0.2 and Mac OS X/GCC 4.0.1 by
Conrad Halling on 26 January 2006. See http://www.bifx.org/SSAHA/index.html
for more information.

1. To compile the main ssaha executable

make ssaha

Once compiled, run ssaha, ssaha -h or ssaha -help to print the help file.

2. To compile test harnesses:

make test

This produces five executables

testHashTable
testHashTableNoOverlap
testQueryManager
testSequenceReaderFasta 
testTimeStamp

all of which should run to completion (may need to do an `unlimit' to
give testHashTableNoOverlap enough memory)

3. To compile the ssaha.a library (necessary to build the SSAHA client and
server in SSAHA/EnsemblServer):

make ssaha.a





