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$Id$

Janda
*****

1. Introduction
===============

This is Janda, a tool to detect structural variants in
whole-genome DNA sequence data.

Janda's homepage is:

    http://janda.sourceforge.net/

See file NEWS for a description of recent changes to Janda.

Janda is Free Software and distributed under the GNU General Public
License (version 3 or later). See file COPYING for more details.

2. Requirements
===============

To build janda you need to have cxx11 compatible compiler
available. If your default compiler is not supporting cxx11, the
configure script will try different switches to turn on cxx11.

You need to have yat version 0.22 (or later) installed. yat is
available from https://sourceforge.net/projects/libyat/


3. Installation
===============

Janda follows the standard GNU installation procedure.  Please see the
INSTALL file for detailed generic instruction how to build Janda. For
details on specific configure options please see section 'Configure
Options' below.

In brief, the following series of shell commands should configure,
build and install janda:

  $ ./configure [OPTIONS]

  $ make

  $ make install

  $ make installcheck


4. Configure Options
====================

* --with-yat: Configure script uses the 'yat-config' script to
    retrieve information how to build against yat library. If
    'yat-config' is not available in your PATH, you may guide
    configure to find 'yat-config' with for example:

    $ ./configure --with-yat=/opt/local/bin/yat-config

* CPPFLAGS: If you have header files installed in a non-standard
  location you can help the preprocessor to find header files using
  CPPFLAGS. If you, for example, have header files available in
  '/opt/local/include', you can run configure as:

    $ ./configure CPPFLAGS=-I/opt/local/include

* LDFLAGS: If you have libraries installed in a non-standard
  location you can help the linker to find libraries using
  LDFLAGS. If you, for example, have libraries available in
  '/opt/local/lib', you can run configure as:

    $ ./configure LDFLAGS=-L/opt/local/lib


5. Reporting Bugs
=================

If you find a bug, please send a report to
<janda-help@lists.sourceforge.net>.

All bug reports should include:

    * The version number of Janda (and underlying libraries).
    * A desription of the bug behaviour, and expected behaviour.
    * The parameters used when running Janda.

--
  Copyright (C) 2013, 2014, 2015, 2016, 2019, 2021, 2024 Peter Johansson

  This file is part of janda

Copying and distribution of this file, with or without modification,
are permitted in any medium without royalty provided the copyright
notice and this notice are preserved.  This file is offered as-is,
without warranty of any kind.