File	Date	Author	Commit
HyLiTE_manuscript	2013-09-05	Wandrille Duchemin	[fadaf6] updated manuscript and supp material
doc	2018-08-03	Murray Cox	[66f8bc] Update website links
example	2018-01-10	Murray Cox	[b9bc60] Add example zip files
false_testing_data	2013-06-19	Wandrille Duchemin	[a80181] HyLiTE version 0.2\n - Fixed the problem result...
src	2018-04-19	Murray Cox	[6a2092] Building wheel for new version
test	2018-01-09	Murray Cox	[e07478] Test passed version 2.0
.gitignore	2018-08-17	Murray Cox	[3cf896] Update gitignore file
HyLiTE_technical_note.pdf	2015-06-30	Pierre-Yves Dupont	[8b89d7] Version 1.6.0. The new version outputs all gene...
LICENSE	2015-07-27	Pierre-Yves Dupont	[10c100] Initial commit
README.txt	2018-04-19	Murray Cox	[a04124] Added bug fix information
test_diploid.zip	2014-02-25	Pierre-Yves Dupont	[95fba5] Bug fixes in the reading of the protocol file

Read Me

(c) Copyright 2013-2018 Murray Cox, Wandrille Duchemin, Pierre-Yves Dupont.


This file is part of HyLiTE.

HyLiTE is a free software: you can redistribute it and/or modify it under the terms of the GNU General Public License version 3 as published by the Free Software Foundation.

HyLiTE 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 License for more details.

You should have received a copy of the GNU General Public License along with HyLiTE.  If not, see <http://www.gnu.org/licenses/>.


#===============#
# HyLiTE Readme #
#===============#

Please visit <hylite.sourceforge.net>.
It contains a lot of useful things, including a tutorial and details about how HyLiTE works.
Thank you for using HyLiTE.
Bugs can be reported here: https://sourceforge.net/p/hylite/tickets/


Release notes:
==============

- 2.0.1: Fixed a bug where lines with spaces rather than tabs in the configuration file were silently ignored

- 2.0.0: Code refactored for Python 3

- 1.7.1: Fix a bug stopping HyLiTE from working in non verbose mode. Works with the new version of samtools 1.2.+

- 1.6.3: Fix a bug in HyLiTE-merge (see ticket https://sourceforge.net/p/hylite/tickets/6/). Need to provide a fasta reference file also for HyLiTE-merge (to build the summary files)

- 1.6.2: Fix a problem in the run summary file (see https://sourceforge.net/p/hylite/tickets/3/). Check that the files entered in the protocol file are valid (they must exist and a warning is returned if they don't seem to be of the right type)

- 1.6.1: Fix the KeyError 'N' bug. It used to occur when a base N is found in the pileup file.

- 1.6.0: Change in the output. Now the summary output files contain all the genes of the reference file, making the comparison of different experiments on the same organism easier to compare. A new subversion number has been given to have a clear separation with the version of the software used in the published work.

- 1.5.4: Version used for the article: HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species. Wandrille Duchemin, Pierre-Yves Dupont, Matthew A Campbell, Austen RD Ganley and Murray P Cox. BMC Bioinformatics 2015, 16:8. doi:10.1186/s12859-014-0433-8