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<h3>
Steffen Möller 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/ee93fa0bfd57aea1ee69170a778a655be7c0ea90">ee93fa0b</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-08-30T18:25:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cosmetics.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqwish/-/commit/4f04e125c5095fe1e1410e8dc6a3e80e4721ef43">4f04e125</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-08-30T18:26:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqwish/-/commit/d133ab50e5795f04776d0da701b05c11bba69938">d133ab50</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-08-30T18:26:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.7.1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqwish/-/commit/dbed67e1224ad194c258bf7c301a7979d0f0df29">dbed67e1</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-08-30T18:26:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.7.1'
Update to upstream version '0.7.1'
with Debian dir fad427772418b13715a7d6e42e850b1919e1753b</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqwish/-/commit/f70bd82ee3d16a977fb1215cf7da755cdb7570df">f70bd82e</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-08-30T21:08:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">(cow-)builds.
</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">
.gitmodules
</a>
</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
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</li>
<li class="file-stats">
<a href="#ee54dc79014b3def963898e50c98877d46c6b27e">
debian/patches/use_debian_packaged_libs.patch
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
<li class="file-stats">
<a href="#c5ae3d305fb0fe15ee61c16c4f258fcf5366521e">
<span class="new-file">
+
debian/seqwish.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#3b17eef8ffd724c7689997905653348f319cf1a9">
src/alignments.cpp
</a>
</li>
<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
</a>
</li>
<li class="file-stats">
<a href="#5ef37652042d6f562ab179ad3a5000d1443a220c">
src/seqindex.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">
<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44"><strong>.gitmodules</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" 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">@@ -7,9 +7,6 @@</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">[submodule "deps/iitii"]</span>
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<td class="new_line diff-line-num" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> path = deps/iitii</span>
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<td class="old_line diff-line-num" data-linenumber="9" 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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<td class="new_line diff-line-num" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> url = https://github.com/ekg/iitii.git</span>
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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">[submodule "deps/mmap_allocator"]</span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> path = deps/mmap_allocator</span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> url = https://github.com/ekg/mmap_allocator.git</span>
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<td class="old_line diff-line-num" data-linenumber="13" 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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<td class="new_line diff-line-num" data-linenumber="10" 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="LC10" class="line" lang="plaintext">[submodule "deps/sdsl-lite"]</span>
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<td class="old_line diff-line-num" data-linenumber="14" 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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<td class="new_line diff-line-num" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> path = deps/sdsl-lite</span>
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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> url = https://github.com/simongog/sdsl-lite.git</span>
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<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" 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="8" 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">@@ -8,7 +8,7 @@ before_install:</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git submodule update --init --recursive</span></span>
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<td class="old_line diff-line-num" data-linenumber="9" 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="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get update -qq</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get install -qq gcc-9 g++-9</span></span>
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<td class="old_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get install -qq gcc-9 g++-9<span class="idiff left right"> libjemalloc-dev</span></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-9</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">sed -i 's/CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -mcx16 -g/CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O -mcx16 -g -fsanitize=address/g' CMakeLists.txt</span></span>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</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">@@ -77,14 +77,6 @@ ExternalProject_Add(iitii</td>
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<pre style="margin: 0;"> <span id="LC77" 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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<pre style="margin: 0;"> <span id="LC78" 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;">${</span><span class="nv" style="color: #008080;">SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/src"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Add</span><span class="p">(</span>mmap_allocator</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cmake"> SOURCE_DIR <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</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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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cmake"> CMAKE_ARGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_ARGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">;-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>"</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cmake"> UPDATE_COMMAND <span class="s2" style="color: #d14;">""</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Get_property</span><span class="p">(</span>mmap_allocator INSTALL_DIR<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>mmap_allocator_INCLUDE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</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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<pre style="margin: 0;">-<span id="LC86" 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;">${</span><span class="nv" style="color: #008080;">INSTALL_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/lib"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># In-place Parallel Super Scalar Samplesort (IPS⁴o), header only</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Add</span><span class="p">(</span>ips4o</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cmake"> SOURCE_DIR <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -184,7 +176,6 @@ add_dependencies(seqwish sdsl-lite)</td>
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184
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_dependencies</span><span class="p">(</span>seqwish gzipreader<span class="p">)</span></span>
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185
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_dependencies</span><span class="p">(</span>seqwish mmmulti<span class="p">)</span></span>
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186
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_dependencies</span><span class="p">(</span>seqwish iitii<span class="p">)</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_dependencies</span><span class="p">(</span>seqwish mmap_allocator<span class="p">)</span></span>
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188
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_dependencies</span><span class="p">(</span>seqwish ips4o<span class="p">)</span></span>
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189
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_dependencies</span><span class="p">(</span>seqwish bbhash<span class="p">)</span></span>
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190
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_dependencies</span><span class="p">(</span>seqwish atomicbitvector<span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="200" 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="191" 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">@@ -200,7 +191,6 @@ target_include_directories(seqwish PUBLIC</td>
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200
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ips4o_INCLUDE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
201
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">mmmulti_INCLUDE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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202
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">iitii_INCLUDE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">mmap_allocator_INCLUDE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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204
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">bbhash_INCLUDE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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205
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">atomicbitvector_INCLUDE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="old_line diff-line-num" data-linenumber="206" 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">
206
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">atomicqueue_INCLUDE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -211,9 +201,9 @@ target_link_libraries(seqwish</td>
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211
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">sdsl-lite_LIB</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/libsdsl.a"</span></span>
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212
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">sdsl-lite-divsufsort_LIB</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/libdivsufsort.a"</span></span>
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213
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">sdsl-lite-divsufsort_LIB</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/libdivsufsort64.a"</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">mmap_allocator_LIB</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/libmmap_allocator.a"</span></span>
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215
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"-latomic"</span></span>
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216
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cmake"> Threads::Threads</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cmake"> jemalloc</span>
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217
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cmake"> z<span class="p">)</span></span>
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>BUILD_STATIC<span class="p">)</span></span>
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219
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#set(CMAKE_EXE_LINKER_FLAGS "-static")</span></span>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">seqwish (0.7-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">seqwish (0.7<span class="idiff left right">.1</span>-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> TODO:</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> [submodule "deps/gzip_reader"] -> missing</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> path = deps/gzip_reader</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> url = https://github.com/gatoravi/gzip_reader.git</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> [ routine-update ]</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.5.1</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">@@ -15,4 +11,10 @@ seqwish (0.7-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> -- Steffen Möller <moeller@debian.org> Sun, 20 Jun 2021 23:28:06 +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Missing dependencies:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> ska</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> mio</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Mon, 30 Aug 2021 18:26:01 +0200</span></pre>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: seqwish</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Steffen Moeller <moeller@debian.org></span>
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<td class="old_line diff-line-num" data-linenumber="4" 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">
4
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<td class="new_line diff-line-num" data-linenumber="5" 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">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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5
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<td class="new_line diff-line-num" data-linenumber="6" 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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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6
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<td class="new_line diff-line-num" data-linenumber="7" 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">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="old_line diff-line-num" data-linenumber="7" 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">
7
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<td class="new_line diff-line-num" data-linenumber="8" 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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> cmake,</span>
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<td class="old_line diff-line-num" data-linenumber="8" 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">
8
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<td class="new_line diff-line-num" data-linenumber="9" 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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libsdsl-dev,</span>
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<td class="old_line diff-line-num" data-linenumber="9" 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">
9
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<td class="new_line diff-line-num" data-linenumber="10" 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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libargs-dev,</span>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="plaintext"> libatomicbitvector-dev,</span>
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<td class="old_line diff-line-num" data-linenumber="10" 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">
10
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<td class="new_line diff-line-num" data-linenumber="12" 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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libatomic-queue-dev,</span>
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<td class="old_line diff-line-num" data-linenumber="11" 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">
11
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<td class="new_line diff-line-num" data-linenumber="13" 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">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libbbhash-dev,</span>
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<td class="old_line diff-line-num" data-linenumber="12" 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">
12
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<td class="new_line diff-line-num" data-linenumber="14" 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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libflathashmap-dev,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="16" 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">@@ -14,8 +16,11 @@ Build-Depends: debhelper-compat (= 13),</td>
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14
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<td class="new_line diff-line-num" data-linenumber="16" 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">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libiitii-dev,</span>
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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
15
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<td class="new_line diff-line-num" data-linenumber="17" 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">
17
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> libips4o-dev,</span>
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<td class="old_line diff-line-num" data-linenumber="16" 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">
16
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<td class="new_line diff-line-num" data-linenumber="18" 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">
18
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> libmmmulti-dev,</span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> libparyfor-dev</span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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<td class="old_line diff-line-num new" 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">
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<td class="new_line diff-line-num new" 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="plaintext"> libparyfor-dev,</span>
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<td class="old_line diff-line-num new" 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">
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<td class="new_line diff-line-num new" 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="plaintext"> libomp-dev,</span>
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<td class="old_line diff-line-num new" 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">
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<td class="new_line diff-line-num new" 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="plaintext"> zlib1g-dev,</span>
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<td class="old_line diff-line-num new" 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">
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<td class="new_line diff-line-num new" 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="plaintext"> libjemalloc-dev</span>
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<td class="old_line diff-line-num new" 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">
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<td class="new_line diff-line-num new" data-linenumber="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Standards-Version: 4.6.0</span>
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<td class="old_line diff-line-num" data-linenumber="19" 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">
19
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<td class="new_line diff-line-num" data-linenumber="24" 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">
24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/seqwish</span>
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<td class="old_line diff-line-num" data-linenumber="20" 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">
20
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<td class="new_line diff-line-num" 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">
25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/seqwish.git</span>
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<td class="old_line diff-line-num" data-linenumber="21" 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">
21
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<td class="new_line diff-line-num" 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="plaintext">Homepage: https://github.com/ekg/seqwish</span>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">grep </span>Description debian/control | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f2</span> <span class="nt" style="color: #000080;">-d</span>:<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">grep</span> ^Version | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f2</span> <span class="nt" style="color: #000080;">-d</span><span class="s1" style="color: #d14;">' '</span>| <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1</span> <span class="nt" style="color: #000080;">-d-</span><span class="si" style="color: #d14;">)</span> <span class="nt" style="color: #000080;">-s</span> 1 <span class="nt" style="color: #000080;">--no-discard-stderr</span> bin/seqwish <span class="o" style="font-weight: 600;">></span> debian/seqwish.1</span></pre>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/seqwish.1</span></pre>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#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">@@ -45,8 +45,8 @@ Index: seqwish/CMakeLists.txt</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> ExternalProject_Get_property(gzipreader SOURCE_DIR)</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> set(gzipreader_INCLUDE "${SOURCE_DIR}")</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else()</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("Use Debian packaged libgzipreader")</span></span>
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<pre style="margin: 0;">-<span id="LC49" 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="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("Use Debian packaged lib<span class="idiff left">gzstream-dev, aka </span>gzip<span class="idiff right">_</span>reader")</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("=================================<span class="idiff left right">===================</span>")</span></span>
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<pre style="margin: 0;"> <span id="LC50" 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="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# add_custom_target(libgzipreader)</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></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">@@ -70,22 +70,7 @@ Index: seqwish/CMakeLists.txt</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> # iitii, like cgranges but with interpolation and memory mapping</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> ExternalProject_Add(iitii</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/iitii"</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="p">@@ -84,7 +113,14 @@</span> ExternalProject_Add(mmap_allocator</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> ExternalProject_Get_property(mmap_allocator INSTALL_DIR)</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"> set(mmap_allocator_INCLUDE "${INSTALL_DIR}/include/mmap_allocator")</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"> set(mmap_allocator_LIB "${INSTALL_DIR}/lib")</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else()</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("Use Debian packaged libiitii (implicitly injecting mmap_allocator)")</span></span>
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<pre style="margin: 0;">-<span id="LC79" 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="LC80" 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="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# add_custom_target(libiitii)</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC84" 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="LC85" class="line" lang="diff"> # In-place Parallel Super Scalar Samplesort (IPS⁴o), header only</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> ExternalProject_Add(ips4o</span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/ips4o"</span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="p">@@ -113,7 +149,9 @@</span> ExternalProject_Add(atomicbitvector</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -105,7 +134,9 @@</span> ExternalProject_Add(atomicbitvector</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> CONFIGURE_COMMAND "")</span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> ExternalProject_Get_property(atomicbitvector SOURCE_DIR)</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> set(atomicbitvector_INCLUDE "${SOURCE_DIR}/include")</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,16 +80,78 @@ Index: seqwish/CMakeLists.txt</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> # atomic queue library</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> ExternalProject_Add(atomicqueue</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/atomic_queue"</span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">23,6</span> +16<span class="idiff">1</span>,1<span class="idiff right">2</span> @@</span> ExternalProject_Add(atomicqueue</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">15,7</span> +1<span class="idiff">4</span>6,1<span class="idiff right">4</span> @@</span> ExternalProject_Add(atomicqueue</span>
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99
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"> CONFIGURE_COMMAND "")</span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"> ExternalProject_Get_property(atomicqueue SOURCE_DIR)</span>
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101
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> set(atomicqueue_INCLUDE "${SOURCE_DIR}")</span>
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102
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else()</span></span>
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103
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("Use Debian packaged atomicqueue")</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("===============================<span class="idiff left right">===================================</span>")</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("===============================")</span></span>
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105
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# FIXME: Not yet tested</span></span>
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106
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# add_custom_target(libatomic-queue)</span></span>
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107
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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108
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="diff"> </span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(!DEBIAN_BUILD)</span></span>
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109
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> # ska</span>
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110
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="diff"> ExternalProject_Add(ska</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/flat_hash_map"</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="p">@@ -125,7 +163,12 @@</span> ExternalProject_Add(ska</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> CONFIGURE_COMMAND "")</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> ExternalProject_Get_property(ska SOURCE_DIR)</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> set(ska_INCLUDE "${SOURCE_DIR}")</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else()</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("Use Debian packaged flat_hash_map")</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("=================================")</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(!DEBIAN_BUILD)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> # paryfor parallel_for</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> ExternalProject_Add(paryfor</span>
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<td class="new_line diff-line-num new" data-linenumber="110" 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">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> #GIT_REPOSITORY "https://github.com/ekg/paryfor"</span>
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<td class="new_line diff-line-num new" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="p">@@ -137,7 +180,12 @@</span> ExternalProject_Add(paryfor</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> CONFIGURE_COMMAND "")</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> ExternalProject_Get_property(paryfor SOURCE_DIR)</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> set(paryfor_INCLUDE "${SOURCE_DIR}")</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else()</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("Use Debian packaged paryfor")</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("===========================")</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> </span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(!DEBIAN_BUILD)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> #add_subdirectory(deps/mmmulti/deps/mio)</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> ExternalProject_Add(mio</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/mmmulti/deps/mio"</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="p">@@ -147,6 +195,10 @@</span> ExternalProject_Add(mio</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> CONFIGURE_COMMAND "")</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> ExternalProject_Get_property(mio SOURCE_DIR)</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> set(mio_INCLUDE "${SOURCE_DIR}/include")</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else()</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("Use Debian packaged mio")</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("=======================")</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> #set(CMAKE_BUILD_TYPE Debug)</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> set(CMAKE_BUILD_TYPE Release)</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="p">@@ -198,16 +250,18 @@</span> target_include_directories(seqwish PUBLI</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> "${paryfor_INCLUDE}"</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> "${mio_INCLUDE}")</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> target_link_libraries(seqwish</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "${sdsl-lite_LIB}/libsdsl.a"</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a"</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a"</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "-lsdsl"</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "-ldivsufsort"</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "-ldivsufsort64"</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> "-latomic"</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "-lgzstream"</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "-lgomp"</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> Threads::Threads</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> jemalloc</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> z)</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> if (BUILD_STATIC)</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> #set(CMAKE_EXE_LINKER_FLAGS "-static")</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- set(CMAKE_EXE_LINKER_FLAGS "-static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive")</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ set(CMAKE_EXE_LINKER_FLAGS "-Wl,--whole-archive -lpthread -Wl,--no-whole-archive")</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> endif()</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> </span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> install(TARGETS seqwish DESTINATION bin)</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><span class="idiff left right"># </span>DH_VERBOSE := 1</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">#export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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9
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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">export CFLAGS += -I/usr/include/atomic_queue -pthread </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">export CXXFLAGS += -I/usr/include/atomic_queue -pthread </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">export LDFLAGS += -pthread -lgomp</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,10 +17,14 @@ CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo $(CMAKE_EXTRA_FLAGS)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo $(CMAKE_EXTRA_FLAGS)<span class="idiff left right"> || echo "I: Experienced error - ignored"</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">#endif</span></pre>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> dh_auto_test</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> rm -f bin/seqwish</span></pre>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#c5ae3d305fb0fe15ee61c16c4f258fcf5366521e"><strong>debian/seqwish.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SEQWISH "1" "August 2021" "seqwish 0.7.1" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">seqwish \- alignment to variation graph inducer</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.IP</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">bin/seqwish {OPTIONS}</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.IP</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">seqwish: a variation graph inducer</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.IP</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">OPTIONS:</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">display this help menu</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-p[FILE]\fR, \fB\-\-paf\-alns\fR=\fI\,[FILE]\/\fR</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Induce the graph from these PAF</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">formatted alignments. Optionally, a list</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">of filenames and minimum match lengths:</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">[file_1]:[min_match_length_1],... This</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">allows the differential filtering of</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">short matches from some but not all</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">inputs, in effect allowing `\-k` to be</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">specified differently for each input.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-s[FILE]\fR, \fB\-\-seqs\fR=\fI\,[FILE]\/\fR</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">The sequences used to generate the</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">alignments (FASTA, FASTQ, .seq)</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-b[BASE]\fR, \fB\-\-base\fR=\fI\,[BASE]\/\fR</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Build graph using this basename</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-g[FILE]\fR, \fB\-\-gfa\fR=\fI\,[FILE]\/\fR</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Write the graph in GFA to FILE</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-m[FILE]\fR, \fB\-\-match\-list\fR=\fI\,[FILE]\/\fR</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Use the sequence match list in FILE to</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">subset the input alignments</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-o[BASE]\fR, \fB\-\-vgp\-out\fR=\fI\,[BASE]\/\fR</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Write the graph in VGP format with</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">basename FILE</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-t[N]\fR, \fB\-\-threads\fR=\fI\,[N]\/\fR</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Use this many threads during parallel</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">steps</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-r[N]\fR, \fB\-\-repeat\-max\fR=\fI\,[N]\/\fR</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Limit transitive closure to include no</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">more than N copies of a given input base</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.TP</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-l[N]\fR, \fB\-\-min\-repeat\-distance\fR=\fI\,[N]\/\fR</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">Prevent transitive closure for bases at</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">least this far apart in input sequences</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.TP</span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">\fB\-k[N]\fR, \fB\-\-min\-match\-len\fR=\fI\,[N]\/\fR</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Filter exact matches below this length.</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">This can smooth the graph locally and</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">prevent the formation of complex local</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">graph topologies from forming due to</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">differential alignments.</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.TP</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">\fB\-B[N]\fR, \fB\-\-transclose\-batch\fR=\fI\,[N]\/\fR</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">Number of bp to use for transitive</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">closure batch (default 1M)</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.TP</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">\fB\-T\fR, \fB\-\-keep\-temp\fR</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">keep intermediate files generated during</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">graph induction</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.TP</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">\fB\-P\fR, \fB\-\-show\-progress\fR</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">log algorithm progress</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.TP</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">\fB\-V\fR, \fB\-\-verbose\-debug\fR</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">enable verbose debugging</span></pre>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#3b17eef8ffd724c7689997905653348f319cf1a9"><strong>src/alignments.cpp</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">@@ -31,6 +31,7 @@ void paf_worker(</td>
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31
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">op</span><span class="p">)</span> <span class="p">{</span></span>
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32
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">:</span></span>
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33
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'='</span><span class="p">:</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'X'</span><span class="p">:</span></span>
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34
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="p">{</span></span>
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35
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">pos_t</span> <span class="n" style="color: #333;">q_pos_match_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_pos</span><span class="p">;</span></span>
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36
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">pos_t</span> <span class="n" style="color: #333;">t_pos_match_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t_pos</span><span class="p">;</span></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">@@ -50,7 +51,10 @@ void paf_worker(</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqidx</span><span class="p">.</span><span class="n" style="color: #333;">at_pos</span><span class="p">(</span><span class="n" style="color: #333;">q_pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seqidx</span><span class="p">.</span><span class="n" style="color: #333;">at_pos</span><span class="p">(</span><span class="n" style="color: #333;">t_pos</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">query_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqidx</span><span class="p">.</span><span class="n" style="color: #333;">at_pos</span><span class="p">(</span><span class="n" style="color: #333;">q_pos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">target_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqidx</span><span class="p">.</span><span class="n" style="color: #333;">at_pos</span><span class="p">(</span><span class="n" style="color: #333;">t_pos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">query_base</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">target_base</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">query_base</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'N'</span></span>
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54
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">offset</span><span class="p">(</span><span class="n" style="color: #333;">q_pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">offset</span><span class="p">(</span><span class="n" style="color: #333;">t_pos</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// guard against self mappings</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">match_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">q_pos_match_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_pos</span><span class="p">;</span></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">@@ -71,10 +75,6 @@ void paf_worker(</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">add_match</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'X'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">incr_pos</span><span class="p">(</span><span class="n" style="color: #333;">q_pos</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">incr_pos</span><span class="p">(</span><span class="n" style="color: #333;">t_pos</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">:</span></span>
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79
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "ins " << c.len << std::endl;</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">incr_pos</span><span class="p">(</span><span class="n" style="color: #333;">q_pos</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#b958235ee8db37bcaceda04b6d55553b450c2db4"><strong>src/main.cpp</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">@@ -80,15 +80,23 @@ int main(int argc, char** argv) {</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[seqwish] ERROR: input alignment file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">paf_alns</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" does not exist"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check if the first non-empty line has the CIGAR</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">igzstream</span> <span class="n" style="color: #333;">paf_in</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">paf_in</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">paf_in</span><span class="p">.</span><span class="n" style="color: #333;">eof</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">paf_in</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">paf_row_t</span> <span class="n" style="color: #333;">paf</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">paf_row_t</span> <span class="n" style="color: #333;">paf</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paf</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()){</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[seqwish] WARNING: input alignment file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" does not have CIGAR strings. "</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"The resulting graph will only represent the input sequences."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paf</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()){</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[seqwish] WARNING: input alignment file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" does not have CIGAR strings. "</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"The resulting graph will only represent the input sequences."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="p">}</span></span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="p">}</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="p">}</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="5ef37652042d6f562ab179ad3a5000d1443a220c">
<a href="https://salsa.debian.org/med-team/seqwish/-/compare/d566dc0d67b8cadf33b597fb124d6d2d97581b46...f70bd82ee3d16a977fb1215cf7da755cdb7570df#5ef37652042d6f562ab179ad3a5000d1443a220c"><strong>src/seqindex.cpp</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">@@ -33,13 +33,11 @@ void seqindex_t::build_index(const std::string& filename, const std::string& idx</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq_bytes_written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seq_names_bytes_written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">notified_empty_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">good</span><span class="p">())</span> <span class="p">{</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">seqname_offset</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">seq_names_bytes_written</span><span class="p">);</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_offset</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">seq_bytes_written</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">;</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">seqnames</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_names_bytes_written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// get the sequence</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">input_is_fasta</span><span class="p">)</span> <span class="p">{</span></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">@@ -52,16 +50,29 @@ void seqindex_t::build_index(const std::string& filename, const std::string& idx</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">input_is_fastq</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// sequence</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">);</span> <span class="idiff left right"> </span><span class="c1" style="color: #998; font-style: italic;">// sequence</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// delimiter</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// quality</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// force the sequence to be upper-case</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">transform</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="p">[](</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="p">});</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">seqout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// record where the sequence starts</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_bytes_written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()){</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">notified_empty_seqs</span><span class="p">){</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">notified_empty_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[seqwish] WARNING: input FASTA file contains empty sequences, which will be ignored."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="p">}</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">seqname_offset</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">seq_names_bytes_written</span><span class="p">);</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_offset</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">seq_bytes_written</span><span class="p">);</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">seqnames</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">seq_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_names_bytes_written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seq_name</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// force the sequence to be upper-case</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">transform</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="p">[](</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="p">});</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">seqout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// record where the sequence starts</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_bytes_written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="p">}</span></span>
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65
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="p">}</span></span>
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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67
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// add the last value so we can get sequence length for the last sequence and name</span></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">@@ -96,7 +107,7 @@ void seqindex_t::build_index(const std::string& filename, const std::string& idx</td>
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96
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">seqnamefile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="old_line diff-line-num" data-linenumber="97" 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="LC108" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">duplicated_ids</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[seqwish] ERROR: <span class="idiff left right">the </span>input sequences have duplicated IDs."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[seqwish] ERROR: input sequences have duplicated IDs."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"></span>
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