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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/pbbam">Debian Med / pbbam</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbbam/commit/e78087f602ca3a1bec888a2307a2b9dcb8d9d05e">e78087f6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-06T11:49:35Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.18.0+dfsg</pre>
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<h4>9 changed files:</h4>
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cmake/FindHTSlib.cmake
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cmake/PbbamTool.cmake
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cmake/pbbam-ccache.cmake
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cmake/pbbam-compilerflags.cmake
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cmake/pbbam-dependencies.cmake
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cmake/pbbam-libtype.cmake
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tools/Darwin/clang-format
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tools/Linux/clang-format
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tools/win32/clang-format.exe
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<h4>Changes:</h4>
<li id="7634cec584cb3ab80ad8821c12dcc759aa942d3d">
<a href="https://salsa.debian.org/med-team/pbbam/commit/e78087f602ca3a1bec888a2307a2b9dcb8d9d05e#7634cec584cb3ab80ad8821c12dcc759aa942d3d"><strong>cmake/FindHTSlib.cmake</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Find HTSlib</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>PkgConfig REQUIRED<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">pkg_check_modules</span><span class="p">(</span>HTSlib REQUIRED htslib<span class="p">)</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># because CMake is trying to be extra clever,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># it will not properly load libraries with</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># absolute paths in *_LIBRARIES</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>HTSlib_LIBRARIES <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">HTSlib_LDFLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">message</span><span class="p">(</span>STATUS <span class="s2" style="color: #d14;">" HTSlib include dirs: </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">HTSlib_INCLUDE_DIRS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">message</span><span class="p">(</span>STATUS <span class="s2" style="color: #d14;">" HTSlib libraries: </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">HTSlib_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span></pre>
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<li id="4e7126818e54ed308c4f1f967280d666c0aeb36c">
<a href="https://salsa.debian.org/med-team/pbbam/commit/e78087f602ca3a1bec888a2307a2b9dcb8d9d05e#4e7126818e54ed308c4f1f967280d666c0aeb36c"><strong>cmake/PbbamTool.cmake</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CMakeParseArguments<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">function</span><span class="p">(</span>create_pbbam_tool<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># parse args</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>oneValueArgs TARGET<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>multiValueArgs SOURCES<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">cmake_parse_arguments</span><span class="p">(</span>create_pbbam_tool <span class="s2" style="color: #d14;">""</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">oneValueArgs</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">multiValueArgs</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">ARGN</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cmake"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># create executable</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">ToolsCommonDir</span><span class="si" style="color: #d14;">}</span> <span class="c1" style="color: #998; font-style: italic;"># shared tool code</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">GeneratedDir</span><span class="si" style="color: #d14;">}</span> <span class="c1" style="color: #998; font-style: italic;"># generated version headers</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">PacBioBAM_INCLUDE_DIRS</span><span class="si" style="color: #d14;">}</span> <span class="c1" style="color: #998; font-style: italic;"># pbbam/htslib includes</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cmake"> <span class="p">)</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">create_pbbam_tool_TARGET</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">create_pbbam_tool_SOURCES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set_target_properties</span><span class="p">(</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cmake"> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">create_pbbam_tool_TARGET</span><span class="si" style="color: #d14;">}</span> PROPERTIES</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cmake"> RUNTIME_OUTPUT_DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">PacBioBAM_BinDir</span><span class="si" style="color: #d14;">}</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake"> <span class="p">)</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">create_pbbam_tool_TARGET</span><span class="si" style="color: #d14;">}</span> pbbam<span class="p">)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cmake"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endfunction</span><span class="p">(</span>create_pbbam_tool<span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pbbam/commit/e78087f602ca3a1bec888a2307a2b9dcb8d9d05e#74d27f873410fce0345b471aeef813dd51a3a1f7"><strong>cmake/pbbam-ccache.cmake</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>PacBioBAM_use_ccache<span class="p">)</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_program</span><span class="p">(</span>CCACHE_FOUND ccache<span class="p">)</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>CCACHE_FOUND<span class="p">)</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set_property</span><span class="p">(</span>GLOBAL PROPERTY RULE_LAUNCH_COMPILE ccache<span class="p">)</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set_property</span><span class="p">(</span>GLOBAL PROPERTY RULE_LAUNCH_LINK ccache<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pbbam/commit/e78087f602ca3a1bec888a2307a2b9dcb8d9d05e#c0ba31cce652e9610d98f43a92d43c475fd5fddb"><strong>cmake/pbbam-compilerflags.cmake</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CheckCXXCompilerFlag<span class="p">)</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># C++11 check & enabling</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>CMAKE_VERSION VERSION_LESS <span class="s2" style="color: #d14;">"3.1"</span><span class="p">)</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_COMPILER_ID</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span> MATCHES <span class="s2" style="color: #d14;">"Clang"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -stdlib=libc++"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># clang</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -std=c++11"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># gcc</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># 3.1+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD 14<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD_REQUIRED ON<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># shared CXX flags for src & tests</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>MSVC<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PacBioBAM_CXX_FLAGS <span class="s2" style="color: #d14;">"/Wall"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PacBioBAM_CXX_FLAGS <span class="s2" style="color: #d14;">"-Wall"</span><span class="p">)</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cmake"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># NOTE: -Wno-unused-local-typedefs used to quash clang warnings w/ Boost</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">check_cxx_compiler_flag</span><span class="p">(</span><span class="s2" style="color: #d14;">"-Wno-unused-local-typedefs"</span> HAS_NO_UNUSED_LOCAL_TYPEDEFS<span class="p">)</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>HAS_NO_UNUSED_LOCAL_TYPEDEFS<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PacBioBAM_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">PacBioBAM_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -Wno-unused-local-typedefs"</span><span class="p">)</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">check_cxx_compiler_flag</span><span class="p">(</span><span class="s2" style="color: #d14;">"-Wno-sign-compare"</span> HAS_NO_SIGN_COMPARE<span class="p">)</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>HAS_NO_SIGN_COMPARE<span class="p">)</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PacBioBAM_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">PacBioBAM_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -Wno-sign-compare"</span><span class="p">)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cmake"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Turn on windows-style filepath resolution.</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># We need to add this #define early (not just in the C# SWIG wrapper)</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>WIN32<span class="p">)</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span>-DPBBAM_WIN_FILEPATHS<span class="p">)</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cmake"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># For now, keep @rpath out of install names on OS X, as it causes SWIG</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># tests to fail.</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>APPLE<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_MACOSX_RPATH OFF<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pbbam/commit/e78087f602ca3a1bec888a2307a2b9dcb8d9d05e#255d68e99c391aa9ae8631673eadeef9a98ef65d"><strong>cmake/pbbam-dependencies.cmake</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># pthreads</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>Threads REQUIRED<span class="p">)</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># boost</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>NOT Boost_INCLUDE_DIRS<span class="p">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>Boost REQUIRED<span class="p">)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cmake"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Winsock for htslib on Windows</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>WIN32<span class="p">)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>SOCKET_LIBRARIES <span class="s2" style="color: #d14;">"ws2_32"</span><span class="p">)</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cmake"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># zlib</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT ZLIB_INCLUDE_DIRS OR NOT ZLIB_LIBRARIES<span class="p">)</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>PkgConfig REQUIRED<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">pkg_check_modules</span><span class="p">(</span>ZLIB zlib<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ZLIB_LIBRARIES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">ZLIB_LDFLAGS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ZLIB_LDFLAGS <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">ZLIB_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cmake"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># htslib</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>NOT HTSLIB_INCLUDE_DIRS OR NOT HTSLIB_LIBRARIES<span class="p">)</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>HTSlib<span class="p">)</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>hts_INCLUDE_DIRS <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">HTSlib_INCLUDE_DIRS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>hts_LIBRARIES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">HTSlib_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">()</span> </span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>hts_INCLUDE_DIRS <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">HTSLIB_INCLUDE_DIRS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>hts_LIBRARIES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">HTSLIB_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pbbam/commit/e78087f602ca3a1bec888a2307a2b9dcb8d9d05e#861766dddd97dbf9f6389c1cfd883fa9445b8a42"><strong>cmake/pbbam-libtype.cmake</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># determine if we need a shared lib</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>PacBioBAM_build_shared<span class="p">)</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>BUILD_SHARED_LIBS ON<span class="p">)</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>htslib_build_shared ON CACHE BOOL <span class="s2" style="color: #d14;">"force htslibConfig to export proper library name"</span><span class="p">)</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PB_LIB_MODE SHARED<span class="p">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PB_LIB_SUFFIX <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SHARED_LIBRARY_SUFFIX</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>BUILD_SHARED_LIBS OFF<span class="p">)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PB_LIB_MODE STATIC<span class="p">)</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>PB_LIB_SUFFIX <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_STATIC_LIBRARY_SUFFIX</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cmake"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>WIN32<span class="p">)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># Limit the number of DLLs we will have to bundle</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_SHARED_LINKER_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SHARED_LINKER_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -static-libgcc -static-libstdc++"</span><span class="p">)</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_MODULE_LINKER_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SHARED_LINKER_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -static-libgcc -static-libstdc++"</span><span class="p">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cmake"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cmake"></span></pre>
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