diff --git a/.circleci/config.yml b/.circleci/config.yml index 244a391..ad6d4e3 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -127,7 +127,8 @@ jobs: - run: name: Install dependencies command: | - choco install mingw make --global + choco install -y mingw --version 12.2.0.03042023 --allow-downgrade --global + choco install -y make --global - run: name: Build command: | diff --git a/COPYING b/COPYING index 4656c3d..777ba37 100644 --- a/COPYING +++ b/COPYING @@ -1,6 +1,3 @@ -[Authors Note : CeCILL-B is a "BSD-compatible" license] - ---- CeCILL-B FREE SOFTWARE LICENSE AGREEMENT diff --git a/LICENSE b/LICENSE index 4e97e6b..d77495c 100644 --- a/LICENSE +++ b/LICENSE @@ -1,5 +1,4 @@ -Copyright (c) 2005-2016, Laurent Noe, Lille University, France -All rights reserved. +Copyright (c) 2005-2024, Laurent Noe, Lille University, France Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: @@ -7,5 +6,6 @@ Redistribution and use in source and binary forms, with or without modification, 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/README.rst b/README.rst index d8b4738..f7531a1 100644 --- a/README.rst +++ b/README.rst @@ -168,7 +168,7 @@ IUPAC filtered seeds could challenge minimizer based techniques , then launching the optimization for a starting shape, and with the given probabilities:: - iedera -iupac -s 5,17 -m "RYYNNNNN,RRYNNNNN" -i shuffle -r 10000 -k -z 100 -f `./tam92.py -p 20 -k 1 --gc 50 + iedera -iupac -s 5,17 -m "RYYNNNNN,RRYNNNNN" -i shuffle -r 10000 -k -z 100 -f `./tam92.py -p 20 -k 1 --gc 50` YNYRNNnnNN,RNYRNnnNNN 0.9999961853027 0.912921 0.087079 @@ -242,11 +242,11 @@ on the bernoulli model provided by the file *model_bernoulli_simple_x_xp.txt* :: Tools provided with iedera ~~~~~~~~~~~~~~~~~~~~~~~~~~ -The ``iedera`` binary is located in ``src/iedera``. The scripts ``plot_spaced_seeds.py`` and ``plot_mow_seeds.py`` are provided to plot: +The ``iedera`` binary is located in ``src/iedera``. The scripts ``plot_spaced_seeds.py`` and ``plot_mow_seeds.py`` are provided to plot : + +* the sensitivity for a 1st hit, on alignments generated with a (parameter-free) bernoulli model, +* the frequency for a 1st hit, on alignments generated with an increasing frequency of matches, for a set of given seeds. -* the sensitivity for a 1st hit, on alignments generated with a (parameter-free) bernoulli model, -* the frequency for a 1st hit, on alignments generated with an increasing frequency of matches, -for a set of given seeds. .. image:: plot_spaced_seeds_figure.png :width: 800