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* README of trunks
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Author: Maria Hartmann
Date: 31 May 2013
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* Installation:
As long as the preprocessor directive TEST_MODE is not set, boost_unit_test_framework is not needed. I.e. under this condition, the
program can be compiled without -l boost_unit_test_framework.

* Compile:

make

* execute/run the tool:

./utrrnaseq

* Boost Library:

A version of the boost library (e.g. Boost_1_49_0) must be installed or at least downloaded, for Ubuntu e.g. type "sudo apt-get install libboost-all-dev"
See docs/INSTALL.md (Boost section) for further details, especially for manual installation from sources or installation
without root rights.

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This folder contains the following folders:

* Debug - This folder contains the object and dependency files.

* doc - The file ./doc/utrrnaseq.doxyfile serves as a configuration file for Doxygen.
        The folder ./doc/html and ./doc/latex contain the automatically by Doxygen created files.		
        This folder also contains all the source code and data used for my bachelor thesis and my thesis itself.

* evaluation - This folder contains files used for test, training and evaluation purposes.

* for-test-cases - This folder contains files used as input for the test cases in the BOOST_TEST_SUITEs and some for
                   comparison purposes.

* input - This folder contains all the used input files and additional data files.

* scripts - This folder contains additional Perl-scripts used for evaluation.

* src - This folder contains all the source code of the tool.

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This folder contains the following files:

* output.example - This file serves as an example for the format of the output file.
