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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/seqwish">Debian Med / seqwish</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/seqwish/-/commit/d133ab50e5795f04776d0da701b05c11bba69938">d133ab50</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2021-08-30T18:26:03+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.7.1</pre>
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<h4>6 changed files:</h4>
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<a href="#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">
.gitmodules
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#3b17eef8ffd724c7689997905653348f319cf1a9">
src/alignments.cpp
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<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
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<li class="file-stats">
<a href="#5ef37652042d6f562ab179ad3a5000d1443a220c">
src/seqindex.cpp
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<h4>Changes:</h4>
<li id="7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">
<a href="https://salsa.debian.org/med-team/seqwish/-/commit/d133ab50e5795f04776d0da701b05c11bba69938#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44"><strong>.gitmodules</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">@@ -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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<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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> url = https://github.com/ekg/iitii.git</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">[submodule "deps/mmap_allocator"]</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> path = deps/mmap_allocator</span>
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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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<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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> path = deps/sdsl-lite</span>
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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/-/commit/d133ab50e5795f04776d0da701b05c11bba69938#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<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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<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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<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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<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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<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/seqwish/-/commit/d133ab50e5795f04776d0da701b05c11bba69938#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;">${</span><span class="nv" style="color: #008080;">CMAKE_ARGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">;-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>"</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cmake"> UPDATE_COMMAND <span class="s2" style="color: #d14;">""</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ExternalProject_Get_property</span><span class="p">(</span>mmap_allocator INSTALL_DIR<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>mmap_allocator_INCLUDE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</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="diff-line-num unfold js-unfold old_line" data-linenumber="184" 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="176" 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">@@ -184,7 +176,6 @@ add_dependencies(seqwish sdsl-lite)</td>
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184
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176
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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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177
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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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178
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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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180
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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 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;">${</span><span class="nv" style="color: #008080;">ips4o_INCLUDE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</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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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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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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<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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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cmake"> <span class="s2" style="color: #d14;">"-latomic"</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cmake"> Threads::Threads</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cmake"> jemalloc</span>
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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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<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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<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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<li id="3b17eef8ffd724c7689997905653348f319cf1a9">
<a href="https://salsa.debian.org/med-team/seqwish/-/commit/d133ab50e5795f04776d0da701b05c11bba69938#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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<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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<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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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="p">{</span></span>
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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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<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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<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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<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/-/commit/d133ab50e5795f04776d0da701b05c11bba69938#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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91
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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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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/seqwish/-/commit/d133ab50e5795f04776d0da701b05c11bba69938#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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<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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<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="diff-line-num unfold js-unfold old_line" data-linenumber="52" 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">@@ -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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<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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<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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<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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<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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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="p">}</span></span>
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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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<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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<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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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>
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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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<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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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"></span>
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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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<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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<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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<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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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <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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66
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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="diff-line-num unfold js-unfold old_line" data-linenumber="96" 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">@@ -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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97
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"></span>
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98
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109
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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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99
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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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110
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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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100
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111
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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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101
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="p">}</span></span>
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102
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"></span>
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