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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/discosnp">Debian Med / discosnp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/-/commit/19aa94b57c2b2c00797b66f26893ebc9e97cbd9b">19aa94b5</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-12-07T22:31:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjust use_debian_packaged_gatb-core.patch to not include GatbCore
The corresponding GatbCore.cmake file provided in Debian will make
cmake look for embedded copies of gatb-core within discosnp source
code. This embedded copy being excluded on purpose, cmake execution
will fail if this GatbCore.cmake file is included. Actually, all the
settings are already properly set by discosnp CMakeLists.txt file
modified by the patch, and the headers package of gatb-core provides
all the elements needed by discosnp to get gatb-core support, so let's
just remove the `include (GatbCore)`
</pre>
</li>
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<h4>1 changed file:</h4>
<ul>
<li class="file-stats">
<a href="#617a6ef0dc813d1ce3f6df69d5f39b1fc3f73294">
debian/patches/use_debian_packaged_gatb-core.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="617a6ef0dc813d1ce3f6df69d5f39b1fc3f73294">
<a href="https://salsa.debian.org/med-team/discosnp/-/commit/19aa94b57c2b2c00797b66f26893ebc9e97cbd9b#617a6ef0dc813d1ce3f6df69d5f39b1fc3f73294"><strong>debian/patches/use_debian_packaged_gatb-core.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,9 +2,9 @@ Author: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 21 Jan 2019 09:01:19 +0100</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Use cmake input file of Debian packaged gatb-core</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">a</span>/CMakeLists.txt</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -32,8 +32,8 @@</span><span class="idiff left right"> ENDIF()</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">discosnp.orig</span>/CMakeLists.txt</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">discosnp</span>/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -32,8 +32,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> # Define cmake modules directory</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> ################################################################################</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,9 +15,19 @@ Description: Use cmake input file of Debian packaged gatb-core</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> # THIRD PARTIES</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/QHC/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/QHC/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="p">@@ -16,13 +16,15 @@</span> include_directories (src ${gatb-core-in</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -43,9 +43,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> SET (GATB_CORE_EXCLUDE_TESTS 1)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> SET (GATB_CORE_EXCLUDE_EXAMPLES 1)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# GATB CORE</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-include (GatbCore)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> # TOOLS GENERATION</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- discosnp.orig/tools/QHC/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ discosnp/tools/QHC/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -16,13 +16,15 @@</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> file (GLOB_RECURSE ProjectFiles src/*)</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> # we define the artifact to be built: the project binary</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,9 +44,9 @@ Description: Use cmake input file of Debian packaged gatb-core</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> # We copy the project binary to the 'bin' directory</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/tools/kissnp2/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/tools/kissnp2/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="p">@@ -16,14 +16,16 @@</span><span class="idiff left right"> include_directories (src ${gatb-core-in</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">discosnp.orig</span>/tools/kissnp2/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">discosnp</span>/tools/kissnp2/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -16,14 +16,16 @@</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> file (GLOB_RECURSE ProjectFiles src/*)</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> # we define the artifact to be built: the project binary</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,9 +66,9 @@ Description: Use cmake input file of Debian packaged gatb-core</td>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/tools/kissreads2/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/tools/kissreads2/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="p">@@ -16,14 +16,16 @@</span><span class="idiff left right"> include_directories (src ${gatb-core-in</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">discosnp.orig</span>/tools/kissreads2/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">discosnp</span>/tools/kissreads2/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="p">@@ -16,14 +16,16 @@</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> file (GLOB_RECURSE ProjectFiles src/*)</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> </span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> # we define the artifact to be built: the project binary</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,9 +88,9 @@ Description: Use cmake input file of Debian packaged gatb-core</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)</span></span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/tools/read_file_names/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/tools/read_file_names/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="p">@@ -16,14 +16,16 @@</span><span class="idiff left right"> include_directories (src ${gatb-core-in</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">discosnp.orig</span>/tools/read_file_names/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">discosnp</span>/tools/read_file_names/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="p">@@ -16,14 +16,16 @@</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="diff"> file (GLOB_RECURSE ProjectFiles src/*)</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="diff"> # we define the artifact to be built: the project binary</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -100,9 +110,9 @@ Description: Use cmake input file of Debian packaged gatb-core</td>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/tools/create_coverage_h5_file/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/tools/create_coverage_h5_file/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="p">@@ -16,14 +16,16 @@</span><span class="idiff left right"> include_directories (src ${gatb-core-in</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">discosnp.orig</span>/tools/create_coverage_h5_file/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">discosnp</span>/tools/create_coverage_h5_file/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="p">@@ -16,14 +16,16 @@</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="diff"> file (GLOB_RECURSE ProjectFiles src/*)</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"> # we define the artifact to be built: the project binary</span>
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