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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqwish">Debian Med / seqwish</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqwish/-/commit/58354c561fd36007b62a4e1c9e12d99a4c6f0fc0">58354c56</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-09T23:05:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depends: libiitii-dev
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqwish/-/commit/4ba6ba4a7654157a724c2178a31ba95ef8045de7">4ba6ba4a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-09T23:22:12+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use Debian packaged iitii, add more todo links
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#ee54dc79014b3def963898e50c98877d46c6b27e">
debian/patches/use_debian_packaged_libs.patch
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</li>
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d22cd37f6eb2e5980516aabd2b05ea3bbb969523...4ba6ba4a7654157a724c2178a31ba95ef8045de7#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" 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">@@ -25,6 +25,7 @@ include_directories("${PROJECT_SOURCE_DIR}")</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Add external projects</span></span>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_ROOT</span><span class="si" style="color: #d14;">}</span>/Modules/ExternalProject.cmake<span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="27" 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">
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="28" 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="LC28" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>!DEBIAN_BUILD<span class="p">)</span></span>
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28
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<td class="diff-line-num new_line" data-linenumber="29" 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">
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># sdsl-lite (full build using its cmake config)</span></span>
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29
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<td class="diff-line-num new_line" data-linenumber="30" 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">
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Add</span><span class="p">(</span>sdsl-lite</span>
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30
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<td class="diff-line-num new_line" data-linenumber="31" 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">
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cmake"> SOURCE_DIR <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/deps/sdsl-lite"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,6 +37,11 @@ set(sdsl-lite_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/include")</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>sdsl-lite-divsufsort_INCLUDE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">INSTALL_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/src/sdsl-lite-build/external/libdivsufsort/include"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>sdsl-lite_LIB <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">INSTALL_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/src/sdsl-lite-build/lib"</span><span class="p">)</span></span>
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<td class="diff-line-num new_line" data-linenumber="39" 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">
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>sdsl-lite-divsufsort_LIB <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">INSTALL_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/src/sdsl-lite-build/external/libdivsufsort/lib"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="40" 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="LC40" 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="41" 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="LC41" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">message</span><span class="p">(</span><span class="s2" style="color: #d14;">"Use Debian packaged sdsl-lite"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">message</span><span class="p">(</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="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">
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># FIXME: Not yet tested</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># add_custom_target(libsdsl)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># taywee's C++ args library, header only</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Add</span><span class="p">(</span>tayweeargs</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">@@ -52,6 +58,7 @@ ExternalProject_Add(gzipreader</td>
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52
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cmake"> INSTALL_COMMAND <span class="s2" style="color: #d14;">""</span><span class="p">)</span></span>
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53
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<td class="diff-line-num new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Get_property</span><span class="p">(</span>gzipreader SOURCE_DIR<span class="p">)</span></span>
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54
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>gzipreader_INCLUDE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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55
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cmake"></span>
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56
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># mmmulti (memory mapped multimap, multiset, and interval tree)</span></span>
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57
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Add</span><span class="p">(</span>mmmulti</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="70" 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">@@ -63,6 +70,7 @@ ExternalProject_Add(mmmulti</td>
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63
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Get_property</span><span class="p">(</span>mmmulti SOURCE_DIR<span class="p">)</span></span>
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64
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>mmmulti_INCLUDE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/src"</span><span class="p">)</span></span>
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65
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cmake"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>!DEBIAN_BUILD<span class="p">)</span></span>
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66
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># iitii, like cgranges but with interpolation and memory mapping</span></span>
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67
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Add</span><span class="p">(</span>iitii</span>
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68
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cmake"> SOURCE_DIR <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/deps/iitii"</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="80" 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">@@ -72,6 +80,7 @@ ExternalProject_Add(iitii</td>
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72
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cmake"> CONFIGURE_COMMAND <span class="s2" style="color: #d14;">""</span><span class="p">)</span></span>
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73
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Get_property</span><span class="p">(</span>iitii SOURCE_DIR<span class="p">)</span></span>
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74
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>iitii_INCLUDE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/src"</span><span class="p">)</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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75
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cmake"></span>
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76
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Add</span><span class="p">(</span>mmap_allocator</span>
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77
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cmake"> SOURCE_DIR <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/deps/mmap_allocator"</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="90" 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">@@ -81,6 +90,7 @@ ExternalProject_Get_property(mmap_allocator INSTALL_DIR)</td>
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81
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>mmap_allocator_INCLUDE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">INSTALL_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/include/mmap_allocator"</span><span class="p">)</span></span>
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82
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>mmap_allocator_LIB <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">INSTALL_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/lib"</span><span class="p">)</span></span>
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83
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cmake"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>!DEBIAN_BUILD<span class="p">)</span></span>
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84
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># In-place Parallel Super Scalar Samplesort (IPS⁴o), header only</span></span>
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85
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<td class="diff-line-num new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Add</span><span class="p">(</span>ips4o</span>
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<td class="diff-line-num old_line" data-linenumber="86" 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">
86
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cmake"> SOURCE_DIR <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/deps/ips4o"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" 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="119" 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">@@ -109,6 +119,7 @@ ExternalProject_Add(atomicbitvector</td>
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109
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cmake"> CONFIGURE_COMMAND <span class="s2" style="color: #d14;">""</span><span class="p">)</span></span>
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110
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Get_property</span><span class="p">(</span>atomicbitvector SOURCE_DIR<span class="p">)</span></span>
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111
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>atomicbitvector_INCLUDE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/include"</span><span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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112
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cmake"></span>
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<td class="diff-line-num old_line" data-linenumber="113" 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">
113
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># atomic queue library</span></span>
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114
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Add</span><span class="p">(</span>atomicqueue</span>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d22cd37f6eb2e5980516aabd2b05ea3bbb969523...4ba6ba4a7654157a724c2178a31ba95ef8045de7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -3,7 +3,8 @@ seqwish (0.6-1) UNRELEASED; urgency=medium</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> TODO:</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * https://github.com/ekg/mmmulti</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> </span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> ... and more</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * https://github.com/max0x7ba/atomic_queue.git</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * https://github.com/skarupke/flat_hash_map</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * https://github.com/ekg/paryfor.git</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sun, 24 May 2020 16:17:07 +0200</span></pre>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d22cd37f6eb2e5980516aabd2b05ea3bbb969523...4ba6ba4a7654157a724c2178a31ba95ef8045de7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libargs-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libatomicbitvector-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libbbhash-dev,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> libiitii-dev,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libips4o-dev,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libgzstream-dev</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d22cd37f6eb2e5980516aabd2b05ea3bbb969523...4ba6ba4a7654157a724c2178a31ba95ef8045de7#ee54dc79014b3def963898e50c98877d46c6b27e"><strong>debian/patches/use_debian_packaged_libs.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">@@ -8,7 +8,7 @@</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> # sdsl-lite (full build using its cmake config)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> ExternalProject_Add(sdsl-lite</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite"</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -36,<span class="idiff left right">7 +37,14</span> @@</span> set(sdsl-lite_INCLUDE "${INSTALL_DIR}/sr</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -36,<span class="idiff left right">6 +37,11</span> @@</span> set(sdsl-lite_INCLUDE "${INSTALL_DIR}/sr</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> set(sdsl-lite-divsufsort_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/include")</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> set(sdsl-lite_LIB "${INSTALL_DIR}/src/sdsl-lite-build/lib")</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> set(sdsl-lite-divsufsort_LIB "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/lib")</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">@@ -17,33 +17,46 @@</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("=================================")</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# FIXME: Not yet tested</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;">+# add_custom_target(libsdsl)</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(!DEBIAN_BUILD)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> # taywee's C++ args library, header only</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> ExternalProject_Add(tayweeargs</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/args"</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -52,6 +60,7 @@</span> ExternalProject_Add(gzipreader</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -52,6 +58,7 @@</span> ExternalProject_Add(gzipreader</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> INSTALL_COMMAND "")</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> ExternalProject_Get_property(gzipreader SOURCE_DIR)</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> set(gzipreader_INCLUDE "${SOURCE_DIR}")</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif<span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> # mmmulti (memory mapped multimap, multiset, and interval tree)</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> ExternalProject_Add(mmmulti</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">90,6 +99,7 @@</span></span><span class="idiff right"> ExternalProject_Add(ips4o</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> ExternalProject_Get_property(<span class="idiff left right">ips4o</span> SOURCE_DIR)</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> set(<span class="idiff left right">ips4o_INCLUDE "${SOURCE_DIR}</span>")</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">63,6 +70,7 @@</span></span><span class="idiff right"> ExternalProject_Add(mmmulti</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> ExternalProject_Get_property(<span class="idiff left right">mmmulti</span> SOURCE_DIR)</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> set(<span class="idiff left right">mmmulti_INCLUDE "${SOURCE_DIR}/src</span>")</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(!DEBIAN_BUILD)</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> # BBHash perfect hasher</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> ExternalProject_Add(bbhash</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/BBHash"</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> # iitii, like cgranges but with interpolation and memory mapping</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> ExternalProject_Add(iitii</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/iitii"</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -72,6 +80,7 @@</span> ExternalProject_Add(iitii</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> CONFIGURE_COMMAND "")</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> ExternalProject_Get_property(iitii SOURCE_DIR)</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> set(iitii_INCLUDE "${SOURCE_DIR}/src")</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> ExternalProject_Add(mmap_allocator</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/mmap_allocator"</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -81,6 +90,7 @@</span> ExternalProject_Get_property(mmap_alloca</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> set(mmap_allocator_INCLUDE "${INSTALL_DIR}/include/mmap_allocator")</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> set(mmap_allocator_LIB "${INSTALL_DIR}/lib")</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(!DEBIAN_BUILD)</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> # In-place Parallel Super Scalar Samplesort (IPS⁴o), header only</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> ExternalProject_Add(ips4o</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/ips4o"</span>
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42
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"><span class="p">@@ -109,6 +119,7 @@</span> ExternalProject_Add(atomicbitvector</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> CONFIGURE_COMMAND "")</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> ExternalProject_Get_property(atomicbitvector SOURCE_DIR)</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> set(atomicbitvector_INCLUDE "${SOURCE_DIR}/include")</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif<span class="idiff left right">()</span></span></span>
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47
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> </span>
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48
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> # atomic queue library</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> ExternalProject_Add(atomicqueue</span></pre>
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