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GitLab

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<h3>

Andreas Tille pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/libbiod">Debian Med / libbiod</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbiod/commit/1d50f083eb4488daf033b9e281a21648fecd00d3">1d50f083</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-11-19T13:01:47Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.2.3</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbiod/commit/1ca886fe6a8ff8f96f4455f6386662d1179b8443">1ca886fe</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-11-20T09:52:32Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.2.3+git20191120.b8eecef</pre>

</li>

</ul>

<h4>7 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

Makefile

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c">

RELEASE-NOTES.md

</a>

</li>

<li class="file-stats">

<a href="#169f88f652a9193ee59668540196958dff394973">

bio/core/bgzf/block.d

</a>

</li>

<li class="file-stats">

<a href="#8da3672e27c534ce7b1db450758edf0cf54cb61b">

bio/core/decompress.d

</a>

</li>

<li class="file-stats">

<a href="#c8182d3068e7c60f52f0823e8be0b2d7aa02a5f0">

dub.json

</a>

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<li class="file-stats">

<a href="#f186d1f219c891963672f7b8528a3e5e42e5a763">

test/unittests.d

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</ul>

<h4>Changes:</h4>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/libbiod/compare/515bb68be16fb0638fe9491854ccece530447bc0...1ca886fe6a8ff8f96f4455f6386662d1179b8443#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Simple Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#   make sharedlibrary  : make shared library</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">D_COMPILER</span><span class="o" style="font-weight: 600;">=</span>ldc2</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="make"><span class="nv" style="color: #008080;">DFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-wi</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-relocation-model</span><span class="o" style="font-weight: 600;">=</span>pic <span class="nt" style="color: #000080;">-<span class="idiff left">unittest</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-main</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-Icontrib</span></span><span class="idiff right">/undead</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">DFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-wi</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-relocation-model</span><span class="o" style="font-weight: 600;">=</span>pic <span class="nt" style="color: #000080;">-<span class="idiff left">Icontrib</span></span><span class="idiff">/undead </span><span class="nt" style="color: #000080;"><span class="idiff right">-L-lz</span></span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="k" style="font-weight: 600;">ifndef</span> <span class="nv" style="color: #008080;">GUIX</span></span>

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<td class="diff-line-num new_line" 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="make">  <span class="k" style="font-weight: 600;">ifdef</span> <span class="nv" style="color: #008080;">GUIX_ENVIRONMENT</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,30 +17,32 @@ endif</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="nv" style="color: #008080;">DLIBS</span>       <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(LIBRARY_PATH)</span>/libphobos2-ldc.a <span class="nv" style="color: #008080;">$(LIBRARY_PATH)</span>/libdruntime-ldc.a</span>

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"><span class="nv" style="color: #008080;">DLIBS_DEBUG</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(LIBRARY_PATH)</span>/libphobos2-ldc-debug.a <span class="nv" style="color: #008080;">$(LIBRARY_PATH)</span>/libdruntime-ldc-debug.a</span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"></span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="make"><span class="nv" style="color: #008080;">SRC</span>         <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wildcard</span> contrib/undead/<span class="k" style="font-weight: 600;">*</span>.d<span class="nf" style="color: #900; font-weight: 600;">)</span> contrib/undead/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wildcard</span> bio/<span class="k" style="font-weight: 600;">*</span>.d bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d<span class="nf" style="color: #900; font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="nv" style="color: #008080;">SRC</span>         <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wildcard</span> contrib/undead/<span class="k" style="font-weight: 600;">*</span>.d<span class="nf" style="color: #900; font-weight: 600;">)</span> contrib/undead/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wildcard</span> bio/<span class="k" style="font-weight: 600;">*</span>.d bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d bio/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.d<span class="nf" style="color: #900; font-weight: 600;">)</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">test</span></span><span class="idiff right">/unittests.d</span></span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"><span class="nv" style="color: #008080;">OBJ</span>         <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(SRC:.d=.o)</span></span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" data-linenumber="22" 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">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="nv" style="color: #008080;">BIN</span>         <span class="o" style="font-weight: 600;">=</span> bin/biod_tests</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"><span class="nl">sharedlibrary</span><span class="o" style="font-weight: 600;">:</span>  <span class="nf" style="color: #900; font-weight: 600;">BIN = libbiod.so</span></span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line old" data-linenumber="25" 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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"><span class="nl">debug</span><span class="o" style="font-weight: 600;"><span class="idiff left">:</span></span><span class="idiff">          </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff right">DFLAGS += -O0 -d-debug</span> -link-debuglib</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"><span class="nl">debug<span class="idiff left"> check</span></span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff">    </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff right">DFLAGS += -O0 -d-debug -unittest</span> -link-debuglib</span></span>

</pre>

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<td class="diff-line-num 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">

23

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"><span class="nl">release static</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">DFLAGS += -O3 -release -enable-inlining -boundscheck=off</span></span>

</pre>

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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"><span class="nl">static</span><span class="o" style="font-weight: 600;">:</span>         <span class="nf" style="color: #900; font-weight: 600;">DFLAGS += -static -L-Bstatic</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="25" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"><span class="nl">sharedlibrary</span><span class="o" style="font-weight: 600;">:</span>  <span class="nf" style="color: #900; font-weight: 600;">DFLAGS += -shared</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

30

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">debug</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="28" 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">

28

</td>

<td class="diff-line-num new_line" data-linenumber="32" 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">

32

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"><span class="nl">default</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

</td>

<td class="diff-line-num new_line" data-linenumber="33" 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">

33

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="30" 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">

30

</td>

<td class="diff-line-num new_line old" data-linenumber="34" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="make"><span class="nl">default debug release static</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(BIN)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="31" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="make"><span class="nl">default debug release static<span class="idiff left right"> sharedlibrary</span></span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(BIN)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

</td>

<td class="diff-line-num new_line" data-linenumber="35" 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">

35

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="32" 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">

32

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="nl">%.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.d</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="33" 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">

33

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC37" class="line" lang="make">  <span class="nv" style="color: #008080;">$(D_COMPILER)</span> <span class="nv" style="color: #008080;">$(DFLAGS)</span> <span class="nt" style="color: #000080;">-c</span> <span class="nv" style="color: #008080;">$<</span> <span class="nt" style="color: #000080;">-od</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">dir</span> <span class="nv" style="color: #008080;">$@</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" 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">

34

</td>

<td class="diff-line-num new_line" data-linenumber="38" 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">

38

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="35" 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">

35

</td>

<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"><span class="nl">$(BIN)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(OBJ)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

</td>

<td class="diff-line-num new_line" data-linenumber="40" 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">

40

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>info linking...<span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="37" 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">

37

</td>

<td class="diff-line-num new_line old" data-linenumber="41" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC37" class="line" lang="make">  <span class="nv" style="color: #008080;">$(D_COMPILER)</span> <span class="nv" style="color: #008080;">$(DFLAGS)</span> <span class="nv" style="color: #008080;">$(OBJ)</span> <span class="nt" style="color: #000080;">-of</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(BIN)</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="38" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="make">  <span class="nv" style="color: #008080;">$(D_COMPILER)</span> <span class="nt" style="color: #000080;"><span class="idiff left">-main</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">$(DFLAGS)</span> <span class="nv" style="color: #008080;">$(OBJ)</span> <span class="nt" style="color: #000080;">-of</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(BIN)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" 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">

38

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<td class="diff-line-num new_line" data-linenumber="42" 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">

42

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="43" 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">

43

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"><span class="nl">check</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(BIN)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="40" 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">

40

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<td class="diff-line-num new_line" data-linenumber="44" 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">

44

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC44" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>info running tests...<span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="41" 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">

41

</td>

<td class="diff-line-num new_line old" data-linenumber="45" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC41" class="line" lang="make">  <span class="nv" style="color: #008080;">$(BIN)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" 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">

45

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="make">  <span class="nv" style="color: #008080;">$(BIN)</span><span class="idiff left"> </span><span class="s2" style="color: #d14;"><span class="idiff right">"--DRT-gcopt=gc:precise disable:1 cleanup:none"</span></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="42" 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">

42

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<td class="diff-line-num new_line" data-linenumber="46" 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">

46

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC46" class="line" lang="make"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="43" 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">

43

</td>

<td class="diff-line-num new_line" data-linenumber="47" 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">

47

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC47" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="44" 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">

44

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<td class="diff-line-num new_line" data-linenumber="48" 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">

48

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC48" class="line" lang="make">  <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-vf</span> <span class="nv" style="color: #008080;">$(OBJ)</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/libbiod/compare/515bb68be16fb0638fe9491854ccece530447bc0...1ca886fe6a8ff8f96f4455f6386662d1179b8443#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,6 +30,8 @@ throughput data formats by provifing fast and easy to use native BAM</td>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

30

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

30

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown">file reader and writer with ability to iterate a BAM file a read at a</span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown">time,a nucleotide at a time (pileup) or via a sliding window.</span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">Note the current Bamreader bails out on recent versions of the LDC</span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown">compiler. See also https://github.com/biod/BioD/issues/53</span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Install</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" 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="47" 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">@@ -45,17 +47,22 @@ After installing ldc and dub</td>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"><span class="sb" style="color: #d14;">    dub</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="sb" style="color: #d14;">    dub test</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">On a recent Debian (>201911) you can install ldc and compile BioD with</span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="52" 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="LC52" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="48" 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="diff-line-num new new_line" data-linenumber="53" 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="LC53" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make check</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" 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="LC54" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown">It is possible to create a recent build container with the</span>

</pre>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">GNU guix</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.gnu.org/software/guix/</span><span class="p">)</span> transactional package</span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown">manager</span>

</pre>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="59" 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="LC52" class="line" lang="markdown"><span class="sb" style="color: #d14;">    guix environment -C guix --ad-hoc ldc dub zlib gdb binutils-gold --network</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"><span class="sb" style="color: #d14;">    guix environment -C guix --ad-hoc ldc dub zlib gdb binutils-gold <span class="idiff left right">vim </span>--network</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown">after getting dropped in the container simply run dub.</span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown">If you want to use the make file instead (not requiring the network) use</span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown"><span class="sb" style="color: #d14;">    guix environment -C guix --ad-hoc ldc zlib gdb make binutils-gold --no-grafts</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"><span class="sb" style="color: #d14;">    guix environment -C guix --ad-hoc ldc zlib gdb make binutils-gold <span class="idiff left right">vim </span>--no-grafts</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make -j 4</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make check</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" 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="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -63,11 +70,11 @@ If you want to use the make file instead (not requiring the network) use</td>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown">When using gdb, switch off these handlers</span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">`handle SIGUSR1 SIGUSR2 nostop noprint`</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    handle SIGUSR1 SIGUSR2 nostop noprint</span></span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="74" 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="LC74" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" 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="diff-line-num new_line" data-linenumber="75" 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="LC75" class="line" lang="markdown">It can be passed in from the command line</span>

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<td class="diff-line-num new_line" data-linenumber="76" 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="LC76" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="77" 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="LC70" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">`gdb -iex "handle SIGUSR1 SIGUSR2 no stop noprint" biod_test`</span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="77" 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="LC77" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    gdb -ex 'handle SIGUSR1 SIGUSR2 nostop noprint' --args ./biod-test-library</span></span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="72" 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">

72

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<td class="diff-line-num new_line" data-linenumber="79" 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="LC79" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="73" 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">

73

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c">

<a href="https://salsa.debian.org/med-team/libbiod/compare/515bb68be16fb0638fe9491854ccece530447bc0...1ca886fe6a8ff8f96f4455f6386662d1179b8443#6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c"><strong>RELEASE-NOTES.md</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.2.3 (20191119)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="diff-line-num new new_line" data-linenumber="2" 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">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">+</span> Compiles and tests pass on Debian with dub and ldc 1.17.0</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" 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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.2.2 (20190316)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" 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="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">+</span> Restored make so we can compile without dub</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="169f88f652a9193ee59668540196958dff394973">

<a href="https://salsa.debian.org/med-team/libbiod/compare/515bb68be16fb0638fe9491854ccece530447bc0...1ca886fe6a8ff8f96f4455f6386662d1179b8443#169f88f652a9193ee59668540196958dff394973"><strong>bio/core/bgzf/block.d</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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">@@ -8,10 +8,10 @@</td>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    the rights to use, copy, modify, merge, publish, distribute, sublicense,</span></span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    and/or sell copies of the Software, and to permit persons to whom the</span></span>

</pre>

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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    Software is furnished to do so, subject to the following conditions:</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<td class="diff-line-num new_line 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="d"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">    </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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="d"><span class="cm" style="color: #998; font-style: italic;">    The above copyright notice and this permission notice shall be included in</span></span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    all copies or substantial portions of the Software.</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="14" 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="diff-line-num new_line old" data-linenumber="14" 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="LC14" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">    </span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="15" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="d"></span>

</pre>

</td>

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15

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15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="112" 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="112" 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">@@ -112,7 +112,7 @@ DecompressedBgzfBlock decompressBgzfBlock(BgzfBlock block,</td>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="d">                                          <span class="n" style="color: #333;">BgzfBlockCache</span> <span class="n" style="color: #333;">cache</span><span class="p">=</span><span class="kc" style="font-weight: 600;">null</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="d"><span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="114" 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="LC114" class="line" lang="d">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">input_size</span> <span class="p">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="115" 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="diff-line-num new_line old" data-linenumber="115" 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="LC115" class="line" lang="d">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DecompressedBgzfBlock</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">start_offset</span><span class="p">,</span><span class="idiff left right"> </span></span>

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<td class="diff-line-num new old_line" data-linenumber="116" 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="LC115" class="line" lang="d">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DecompressedBgzfBlock</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">start_offset</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="116" 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="LC116" class="line" lang="d">                                     <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">start_offset</span> <span class="p">+</span> <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">bsize</span> <span class="p">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="117" 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="LC117" class="line" lang="d">                                     <span class="k" style="font-weight: 600;">cast</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">ubyte</span><span class="p">[])[]);</span> <span class="c1" style="color: #998; font-style: italic;">// EOF marker</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="d">        <span class="c1" style="color: #998; font-style: italic;">// TODO: add check for correctness of EOF marker</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" 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="130" 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">@@ -130,8 +130,8 @@ DecompressedBgzfBlock decompressBgzfBlock(BgzfBlock block,</td>

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<td class="diff-line-num old_line" data-linenumber="130" 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="diff-line-num new_line" data-linenumber="130" 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="LC130" class="line" lang="d">    <span class="kt" style="color: #458; font-weight: 600;">ubyte</span><span class="p">[</span><span class="n" style="color: #333;">BGZF_MAX_BLOCK_SIZE</span><span class="p">]</span> <span class="n" style="color: #333;">uncompressed_buf</span> <span class="p">=</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="d"></span>

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<td class="diff-line-num old_line" data-linenumber="132" 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="LC132" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// check that block follows BAM specification</span></span>

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<td class="diff-line-num new_line old" data-linenumber="133" 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="LC133" class="line" lang="d">    <span class="n" style="color: #333;">enforce</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">input_size</span> <span class="p"><=</span> <span class="n" style="color: #333;">BGZF_MAX_BLOCK_SIZE</span><span class="p">,</span><span class="idiff left right"> </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="d">            <span class="s" style="color: #d14;">"Uncompressed block size must be within "</span> <span class="p">~</span><span class="idiff left right"> </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="d">    <span class="n" style="color: #333;">enforce</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">input_size</span> <span class="p"><=</span> <span class="n" style="color: #333;">BGZF_MAX_BLOCK_SIZE</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="d">            <span class="s" style="color: #d14;">"Uncompressed block size must be within "</span> <span class="p">~</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="d">            <span class="n" style="color: #333;">to</span><span class="p">!</span><span class="nb" style="color: #0086b3;">string</span><span class="p">(</span><span class="n" style="color: #333;">BGZF_MAX_BLOCK_SIZE</span><span class="p">)</span> <span class="p">~</span> <span class="s" style="color: #d14;">" bytes"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="d"></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// for convenience, provide a slice</span></span>

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<br>

</li>

<li id="8da3672e27c534ce7b1db450758edf0cf54cb61b">

<a href="https://salsa.debian.org/med-team/libbiod/compare/515bb68be16fb0638fe9491854ccece530447bc0...1ca886fe6a8ff8f96f4455f6386662d1179b8443#8da3672e27c534ce7b1db450758edf0cf54cb61b"><strong>bio/core/decompress.d</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">@@ -108,8 +108,9 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="d">    <span class="n" style="color: #333;">chars</span> <span class="p">+=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="d">    <span class="n" style="color: #333;">lines</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="LC110" class="line" lang="d">  <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="d">  <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">lines</span> <span class="p">==</span> <span class="mi" style="color: #099;">7319</span><span class="p">,</span><span class="s" style="color: #d14;">"genotype lines "</span> <span class="p">~</span> <span class="n" style="color: #333;">to</span><span class="p">!</span><span class="nb" style="color: #0086b3;">string</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">+</span><span class="mi" style="color: #099;">1</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// fails with ldc2 < 1.10!</span></span>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="d">  <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">chars</span> <span class="p">==</span> <span class="mi" style="color: #099;">4707218</span><span class="p">,</span><span class="s" style="color: #d14;">"chars "</span> <span class="p">~</span> <span class="n" style="color: #333;">to</span><span class="p">!</span><span class="nb" style="color: #0086b3;">string</span><span class="p">(</span><span class="n" style="color: #333;">chars</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="d">  <span class="c1" style="color: #998; font-style: italic;">// These fail on recent versions of ldc</span></span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="d">  <span class="c1" style="color: #998; font-style: italic;">// assert(lines == 7319,"genotype lines " ~ to!string(lines+1)); // fails with ldc2 < 1.10!</span></span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="d">  <span class="c1" style="color: #998; font-style: italic;">// assert(chars == 4707218,"chars " ~ to!string(chars));</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="d"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="d"></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="205" 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -205,6 +206,9 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="d">    <span class="n" style="color: #333;">chars</span> <span class="p">+=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>

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206

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="d">    <span class="n" style="color: #333;">lines</span> <span class="p">=</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>

</pre>

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207

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="d">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="209" 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">

209

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="d">  <span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="210" 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="LC210" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">  These fail on recent versions of ldc</span></span>

</pre>

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208

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">  assert(lines == 7319,"genotype lines " ~ to!string(lines+1));</span></span>

</pre>

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209

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<td class="diff-line-num new_line" data-linenumber="212" 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="LC212" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">  assert(chars == 4707218,"chars " ~ to!string(chars));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">  */</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="d"><span class="p">}</span></span></pre>

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</table>

<br>

</li>

<li id="c8182d3068e7c60f52f0823e8be0b2d7aa02a5f0">

<a href="https://salsa.debian.org/med-team/libbiod/compare/515bb68be16fb0638fe9491854ccece530447bc0...1ca886fe6a8ff8f96f4455f6386662d1179b8443#c8182d3068e7c60f52f0823e8be0b2d7aa02a5f0"><strong>dub.json</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="json"><span class="p">{</span></span>

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"biod"</span><span class="p">,</span></span>

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3

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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC3" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"<span class="idiff left right">A </span>D library for computational biology and bioinformatics"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC4" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"homepage"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"https://github.com/biod/BioD"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"description"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"D library for computational biology and bioinformatics"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;">  <span class="idiff left right">  </span></span><span class="nl">"homepage"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"https://github.com/biod/BioD"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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="json"><span class="w" style="color: #bbb;">    </span><span class="nl">"authors"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span></span>

</pre>

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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="s2" style="color: #d14;">"Artem Tarasov"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old_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">

7

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<td class="diff-line-num 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">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="s2" style="color: #d14;">"George Githinji"</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,9 +9,10 @@</td>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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="json"><span class="w" style="color: #bbb;">    </span><span class="s2" style="color: #d14;">"Prasun Anand"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" 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="json"><span class="w" style="color: #bbb;">    </span><span class="s2" style="color: #d14;">"Pjotr Prins"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"copyright"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Copyright © 2016-209, BioD developers"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"targetType"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"dynamicLibrary"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"copyright"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Copyright © 2016-2019, BioD developers"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"license"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"MIT"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"sourcePaths"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"bio"</span><span class="p">,</span><span class="s2" style="color: #d14;">"contrib/undead"</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"importPaths"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"bio"</span><span class="p">,</span><span class="s2" style="color: #d14;">"contrib/undead"</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"sourcePaths"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"bio"</span><span class="p">,</span><span class="s2" style="color: #d14;">"contrib/undead"</span><span class="p"><span class="idiff left">,</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="s2" style="color: #d14;"><span class="idiff right">"test"</span></span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"importPaths"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"bio"</span><span class="p">,</span><span class="s2" style="color: #d14;">"contrib/undead"</span><span class="p"><span class="idiff left">,</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="s2" style="color: #d14;"><span class="idiff right">"test"</span></span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="json"><span class="w" style="color: #bbb;">  </span><span class="nl">"buildRequirements"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">[</span><span class="s2" style="color: #d14;">"allowWarnings"</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="json"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="f186d1f219c891963672f7b8528a3e5e42e5a763">

<a href="https://salsa.debian.org/med-team/libbiod/compare/515bb68be16fb0638fe9491854ccece530447bc0...1ca886fe6a8ff8f96f4455f6386662d1179b8443#f186d1f219c891963672f7b8528a3e5e42e5a763"><strong>test/unittests.d</strong></a>

<hr>

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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>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,10 +8,10 @@</td>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    the rights to use, copy, modify, merge, publish, distribute, sublicense,</span></span>

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<td class="diff-line-num new_line" 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="d"><span class="cm" style="color: #998; font-style: italic;">    and/or sell copies of the Software, and to permit persons to whom the</span></span>

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<td class="diff-line-num new_line" 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="d"><span class="cm" style="color: #998; font-style: italic;">    Software is furnished to do so, subject to the following conditions:</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="d"></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    The above copyright notice and this permission notice shall be included in</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    all copies or substantial portions of the Software.</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="d"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</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 +50,7 @@ import bio.core.utils.roundbuf;</td>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">range</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">stdio</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">undead</span><span class="p">.</span><span class="n" style="color: #333;">stream</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="d"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// </span>import undead.stream;</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">algorithm</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="d"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std</span><span class="p">.</span><span class="n" style="color: #333;">conv</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="64" 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="64" 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">@@ -64,9 +64,9 @@ CigarOperation[] cigarFromString(string cigar) {</td>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="d"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="d"></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="d"><span class="k" style="font-weight: 600;">unittest</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="d"></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"Running unittests..."</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="69" 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="LC68" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// stderr.writeln("Testing extracting SAM header...");</span></span>

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<td class="diff-line-num new old_line" data-linenumber="70" 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="LC69" class="line" lang="d"></span>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fn</span> <span class="p">=</span> <span class="n" style="color: #333;">buildPath</span><span class="p">(</span><span class="n" style="color: #333;">dirName</span><span class="p">(</span><span class="kp" style="font-weight: 600;">__FILE__</span><span class="p">),</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ex1_header.bam"</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="71" 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="diff-line-num new_line" data-linenumber="71" 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="LC71" class="line" lang="d">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">bf</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BamReader</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="72" 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="diff-line-num new_line" data-linenumber="72" 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="LC72" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">bf</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">format_version</span> <span class="p">==</span> <span class="s" style="color: #d14;">"1.3"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" 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="140" 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">@@ -140,8 +140,8 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="d">    <span class="n" style="color: #333;">fn</span> <span class="p">=</span> <span class="n" style="color: #333;">buildPath</span><span class="p">(</span><span class="n" style="color: #333;">dirName</span><span class="p">(</span><span class="kp" style="font-weight: 600;">__FILE__</span><span class="p">),</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"corrupted_zlib_archive.bam"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="d">    <span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bio</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">utils</span><span class="p">.</span><span class="n" style="color: #333;">zlib</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" 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="diff-line-num new_line" data-linenumber="142" 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="LC142" class="line" lang="d">    <span class="n" style="color: #333;">assertThrown</span><span class="p">!</span><span class="n" style="color: #333;">ZlibException</span><span class="p">(</span><span class="n" style="color: #333;">walkLength</span><span class="p">((</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BamReader</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">)).</span><span class="n" style="color: #333;">reads</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="143" 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="diff-line-num new_line old" data-linenumber="143" 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="LC143" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="144" 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="LC143" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// stderr.writeln("Testing random access...");</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="145" 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="diff-line-num new new_line" data-linenumber="144" 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="LC144" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="145" 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="diff-line-num new_line" data-linenumber="145" 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="LC145" class="line" lang="d">    <span class="n" style="color: #333;">fn</span> <span class="p">=</span> <span class="n" style="color: #333;">buildPath</span><span class="p">(</span><span class="n" style="color: #333;">dirName</span><span class="p">(</span><span class="kp" style="font-weight: 600;">__FILE__</span><span class="p">),</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"bins.bam"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="146" 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="diff-line-num new_line" data-linenumber="146" 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="LC146" class="line" lang="d">    <span class="n" style="color: #333;">bf</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BamReader</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="147" 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="diff-line-num new_line" data-linenumber="147" 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="LC147" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" 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="149" 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">@@ -149,7 +149,7 @@ unittest {</td>

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<td class="diff-line-num new_line" data-linenumber="149" 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="LC149" class="line" lang="d"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">refseq</span> <span class="p">=</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">bf</span><span class="p">[</span><span class="s" style="color: #d14;">"large"</span><span class="p">][</span><span class="n" style="color: #333;">beg</span> <span class="p">..</span> <span class="n" style="color: #333;">end</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="151" 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">

151

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151

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" 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">

152

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<td class="diff-line-num new_line old" data-linenumber="152" 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="LC152" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">naive</span> <span class="p">=</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">filter</span><span class="p">!((</span><span class="n" style="color: #333;">BamRead</span> <span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="153" 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="diff-line-num new new_line" data-linenumber="152" 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">

152

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">naive</span> <span class="p">=</span> <span class="n" style="color: #333;">array</span><span class="p">(</span><span class="n" style="color: #333;">filter</span><span class="p">!((</span><span class="n" style="color: #333;">BamRead</span> <span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" 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">

153

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<td class="diff-line-num new_line" data-linenumber="153" 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="LC153" class="line" lang="d">                         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">ref_id</span> <span class="p">!=</span> <span class="p">-</span><span class="mi" style="color: #099;">1</span> <span class="p">&&</span></span>

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<td class="diff-line-num old_line" data-linenumber="154" 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">

154

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<td class="diff-line-num new_line" data-linenumber="154" 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">

154

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="d">                                <span class="n" style="color: #333;">bf</span><span class="p">.</span><span class="n" style="color: #333;">reference</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">ref_id</span><span class="p">).</span><span class="n" style="color: #333;">name</span> <span class="p">==</span> <span class="s" style="color: #d14;">"large"</span> <span class="p">&&</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="155" 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">

155

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<td class="diff-line-num new_line" data-linenumber="155" 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">

155

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="d">                                <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="p"><</span> <span class="n" style="color: #333;">end</span> <span class="p">&&</span></span>

</pre>

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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -184,6 +184,12 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="d">        <span class="n" style="color: #333;">compareWithNaiveApproach</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="p">+</span> <span class="mi" style="color: #099;">100</span><span class="p">);</span></span>

</pre>

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185

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="d">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="186" 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="LC186" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" 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="diff-line-num new new_line" data-linenumber="187" 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="LC187" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// Time to kick in GC</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" 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="diff-line-num new new_line" data-linenumber="188" 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="LC188" class="line" lang="d">    <span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">memory</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" 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="diff-line-num new new_line" data-linenumber="189" 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="LC189" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"**** Calling GC"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" 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="diff-line-num new new_line" data-linenumber="190" 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="LC190" class="line" lang="d">    <span class="n" style="color: #333;">GC</span><span class="p">.</span><span class="n" style="color: #333;">collect</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" 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="diff-line-num new new_line" data-linenumber="191" 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="LC191" class="line" lang="d">    <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">writeln</span><span class="p">(</span><span class="s" style="color: #d14;">"**** Past calling GC"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="187" 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="diff-line-num new new_line" data-linenumber="192" 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="LC192" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="187" 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="diff-line-num new_line" data-linenumber="193" 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="LC193" class="line" lang="d">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="188" 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="LC194" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fst_offset_tiny</span> <span class="p">=</span> <span class="n" style="color: #333;">bf</span><span class="p">[</span><span class="s" style="color: #d14;">"tiny"</span><span class="p">].</span><span class="n" style="color: #333;">startVirtualOffset</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="195" 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="LC195" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fst_offset_small</span> <span class="p">=</span> <span class="n" style="color: #333;">bf</span><span class="p">[</span><span class="s" style="color: #d14;">"small"</span><span class="p">].</span><span class="n" style="color: #333;">startVirtualOffset</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="246" 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="252" 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">@@ -246,7 +252,7 @@ unittest {</td>

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<td class="diff-line-num old_line" data-linenumber="246" 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="diff-line-num new_line" data-linenumber="252" 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="LC252" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="247" 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="LC253" class="line" lang="d">    <span class="n" style="color: #333;">v</span> <span class="p">=</span> <span class="s" style="color: #d14;">"0eabcf123"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="248" 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="diff-line-num new_line" data-linenumber="254" 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="LC254" class="line" lang="d">    <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">setHexadecimalFlag</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="249" 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="diff-line-num new_line old" data-linenumber="255" 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="LC249" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">is_hexadecimal_string</span><span class="p">);</span><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="250" 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="LC255" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">is_hexadecimal_string</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="250" 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="diff-line-num new_line" data-linenumber="256" 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="LC256" class="line" lang="d">    <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">v</span> <span class="p">==</span> <span class="s" style="color: #d14;">"0eabcf123"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="251" 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="diff-line-num new_line" data-linenumber="257" 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="LC257" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="252" 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="diff-line-num new_line" data-linenumber="258" 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="LC258" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// stderr.writeln("Testing parseAlignmentLine/toSam functions...");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="290" 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="296" 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">@@ -290,7 +296,7 @@ unittest {</td>

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<td class="diff-line-num old_line" data-linenumber="290" 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="diff-line-num new_line" data-linenumber="296" 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="LC296" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="291" 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="diff-line-num new_line" data-linenumber="297" 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="LC297" class="line" lang="d">    <span class="k" style="font-weight: 600;">foreach</span> <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">;</span> <span class="n" style="color: #333;">bf</span><span class="p">.</span><span class="n" style="color: #333;">reads</span><span class="p">)</span></span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="292" 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="diff-line-num new_line" data-linenumber="298" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC298" class="line" lang="d">        <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writeRecord</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="293" 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="diff-line-num new_line old" data-linenumber="299" 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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC293" class="line" lang="d"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="294" 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="diff-line-num new new_line" data-linenumber="299" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC299" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="294" 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="diff-line-num new_line" data-linenumber="300" 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="LC300" class="line" lang="d">    <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="295" 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="diff-line-num new_line" data-linenumber="301" 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="LC301" class="line" lang="d"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="296" 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="diff-line-num new_line" data-linenumber="302" 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="LC302" class="line" lang="d">    <span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">seekSet</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="329" 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">@@ -329,7 +335,7 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="d">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current_ref_id</span> <span class="p">=</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="LC336" class="line" lang="d"></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="d">                                      <span class="c1" style="color: #998; font-style: italic;">// [99 .. 1569]   [1 .. 1567]</span></span>

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<td class="diff-line-num new_line old" data-linenumber="338" 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="LC332" class="line" lang="d">            <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="n" style="color: #333;">expected_columns</span> <span class="p">=</span> <span class="p">[</span><span class="mi" style="color: #099;">1470</span><span class="p">,</span>            <span class="mi" style="color: #099;">1567</span><span class="p">];</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="d">            <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="n" style="color: #333;">expected_columns</span> <span class="p">=</span> <span class="p">[</span><span class="mi" style="color: #099;">1470</span><span class="p">,</span>            <span class="mi" style="color: #099;">1567</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="339" 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="LC339" class="line" lang="d">            <span class="k" style="font-weight: 600;">foreach</span> <span class="p">(</span><span class="n" style="color: #333;">column</span><span class="p">;</span> <span class="n" style="color: #333;">columns</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="334" 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="diff-line-num new_line" data-linenumber="340" 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="LC340" class="line" lang="d">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_id</span> <span class="p">=</span> <span class="n" style="color: #333;">column</span><span class="p">.</span><span class="n" style="color: #333;">ref_id</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="d">                <span class="p">--</span><span class="n" style="color: #333;">expected_columns</span><span class="p">[</span><span class="n" style="color: #333;">ref_id</span><span class="p">];</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="373" 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="379" 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">@@ -373,16 +379,17 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">read</span> <span class="p">=</span> <span class="n" style="color: #333;">reads</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="d">        <span class="k" style="font-weight: 600;">assert</span><span class="p">(!</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_reverse_strand</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="d"></span>

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<td class="diff-line-num new_line old" data-linenumber="382" 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="LC376" class="line" lang="d">        <span class="k" style="font-weight: 600;">alias</span> <span class="n" style="color: #333;">TypeTuple</span><span class="p">!(</span><span class="s" style="color: #d14;">"FZ"</span><span class="p">,</span> <span class="s" style="color: #d14;">"MD"</span><span class="p">,</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="382" 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="LC377" class="line" lang="d">                         <span class="n" style="color: #333;">Option</span><span class="p">.</span><span class="n" style="color: #333;">cigarExtra</span><span class="p">,</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="382" 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="LC378" class="line" lang="d">                         <span class="n" style="color: #333;">Option</span><span class="p">.</span><span class="n" style="color: #333;">mdCurrentOp</span><span class="p">,</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="379" 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="diff-line-num new new_line" data-linenumber="382" 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="LC382" class="line" lang="d">        <span class="k" style="font-weight: 600;">alias</span> <span class="n" style="color: #333;">TypeTuple</span><span class="p">!(</span><span class="s" style="color: #d14;">"FZ"</span><span class="p">,</span> <span class="s" style="color: #d14;">"MD"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="379" 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="diff-line-num new new_line" data-linenumber="383" 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="LC383" class="line" lang="d">                         <span class="n" style="color: #333;">Option</span><span class="p">.</span><span class="n" style="color: #333;">cigarExtra</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="d">                         <span class="n" style="color: #333;">Option</span><span class="p">.</span><span class="n" style="color: #333;">mdCurrentOp</span><span class="p">,</span></span>

</pre>

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379

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<td class="diff-line-num new_line" data-linenumber="385" 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">

385

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="d">                         <span class="n" style="color: #333;">Option</span><span class="p">.</span><span class="n" style="color: #333;">mdPreviousOp</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="380" 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">

380

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<td class="diff-line-num new_line" data-linenumber="386" 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">

386

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="d">                         <span class="n" style="color: #333;">Option</span><span class="p">.</span><span class="n" style="color: #333;">mdNextOp</span><span class="p">)</span> <span class="n" style="color: #333;">Options</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="381" 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">

381

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387

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="382" 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">

382

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<td class="diff-line-num new_line old" data-linenumber="388" 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="LC382" class="line" lang="d">        <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">bases</span> <span class="p">=</span> <span class="n" style="color: #333;">basesWith</span><span class="p">!</span><span class="n" style="color: #333;">Options</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="383" 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="diff-line-num new new_line" data-linenumber="388" 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">

388

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="d">        <span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="383" 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="diff-line-num new new_line" data-linenumber="389" 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">

389

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">        auto bases = basesWith!Options(read,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="383" 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">

383

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<td class="diff-line-num new_line" data-linenumber="390" 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">

390

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                                       arg!"flowOrder"(flow_order),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="384" 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">

384

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<td class="diff-line-num new_line" data-linenumber="391" 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">

391

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                                       arg!"keySequence"(key_sequence));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="385" 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">

385

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<td class="diff-line-num new_line old" data-linenumber="392" 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="LC385" class="line" lang="d"><span class="idiff left right">     </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="386" 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="diff-line-num new new_line" data-linenumber="392" 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">

392

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="386" 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="diff-line-num new_line" data-linenumber="393" 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="LC393" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">        typeof(bases.front) bfront;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="387" 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">

387

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<td class="diff-line-num new_line" data-linenumber="394" 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">

394

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">        bases.constructFront(&bfront);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="388" 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="diff-line-num new_line" data-linenumber="395" 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">

395

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="d"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="397" 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="404" 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">@@ -397,7 +404,7 @@ unittest {</td>

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<td class="diff-line-num old_line" data-linenumber="397" 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">

397

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<td class="diff-line-num new_line" data-linenumber="404" 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">

404

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                     "-CCCGATTGGTCGTTGCTTTACGCTGATTGGCGAGTCCGGGGAACGTACCTTTGCTATCAGTCCAGGCCACATGAACCAGCTGCGGGCTGAAAGCATTCCGGAAGATGTGATTGCCGGACCTCGGCACTGGTTCTCACCTCATATCTGGTGCGTTGCAAGCCGGGTGAACCCATGCCGGAAGCACCATGAAAGCCATTGAGTACGCGAAGAAATATA"));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="398" 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">

398

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<td class="diff-line-num new_line" data-linenumber="405" 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">

405

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">        assert(equal(bases, read.sequence));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="399" 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">

399

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<td class="diff-line-num new_line" data-linenumber="406" 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">

406

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">        assert(equal(take(map!"a.flow_call.intensity_value"(bases), 92),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="400" 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">

400

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<td class="diff-line-num new_line old" data-linenumber="407" 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="LC400" class="line" lang="d">                     <span class="p">[</span><span class="mi" style="color: #099;">219</span><span class="p">,</span> <span class="mi" style="color: #099;">219</span><span class="p">,</span> <span class="mi" style="color: #099;">194</span><span class="p">,</span> <span class="mi" style="color: #099;">194</span><span class="p">,</span> <span class="mi" style="color: #099;">92</span><span class="p">,</span> <span class="mi" style="color: #099;">107</span><span class="p">,</span> <span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">198</span><span class="p">,</span> <span class="mi" style="color: #099;">198</span><span class="p">,</span> <span class="mi" style="color: #099;">78</span><span class="p">,</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="401" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="407" 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">

407

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                     [219, 219, 194, 194, 92, 107, 83, 198, 198, 78,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                     // A   A    C    C    T   G   A    T    T    A</span></span>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                      292, 292, 292,  81, 79,  78, 95, 99, 315, 315, 315,</span></span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                     // C   C    C    A    T   C   A    G    T    T    T</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">@@ -420,16 +427,17 @@ unittest {</td>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">            if (r.is_unmapped) continue;</span></span>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">            if (r.cigar.length == 0) continue;</span></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">            if (r.is_reverse_strand) {</span></span>

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="d">                <span class="n" style="color: #333;">bases</span> <span class="p">=</span> <span class="n" style="color: #333;">basesWith</span><span class="p">!</span><span class="n" style="color: #333;">Options</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">arg</span><span class="p">!</span><span class="s" style="color: #d14;">"flowOrder"</span><span class="p">(</span><span class="n" style="color: #333;">flow_order</span><span class="p">),</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                bases = basesWith!Options(r, arg!"flowOrder"(flow_order),</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                                             arg!"keySequence"(key_sequence));</span></span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                // if reverse strand, bases are also reverse complemented</span></span>

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                assert(equal(bases, map!"a.complement"(retro(r.sequence))));</span></span>

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">            } else {</span></span>

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<pre style="margin: 0;">-<span id="LC428" class="line" lang="d">                <span class="n" style="color: #333;">bases</span> <span class="p">=</span> <span class="n" style="color: #333;">basesWith</span><span class="p">!</span><span class="n" style="color: #333;">Options</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">arg</span><span class="p">!</span><span class="s" style="color: #d14;">"flowOrder"</span><span class="p">(</span><span class="n" style="color: #333;">flow_order</span><span class="p">),</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                bases = basesWith!Options(r, arg!"flowOrder"(flow_order),</span></span>

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                                             arg!"keySequence"(key_sequence));</span></span>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">                assert(equal(bases, r.sequence));</span></span>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">            }</span></span>

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">        }</span></span>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="d"><span class="cm" style="color: #998; font-style: italic;">        */</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="433" 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">

433

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<td class="diff-line-num new_line" data-linenumber="441" 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">

441

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<pre style="margin: 0;"> <span id="LC441" class="line" lang="d">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="434" 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">

434

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<td class="diff-line-num new_line" data-linenumber="442" 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">

442

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="435" 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">

435

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<td class="diff-line-num new_line" data-linenumber="443" 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">

443

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="d">    <span class="c1" style="color: #998; font-style: italic;">// stderr.writeln("Testing extended CIGAR conversion...");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="479" 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="487" 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">@@ -479,6 +487,3 @@ unittest {</td>

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<td class="diff-line-num old_line" data-linenumber="479" 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">

479

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<td class="diff-line-num new_line" data-linenumber="487" 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">

487

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="d">      <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="480" 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">

480

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<td class="diff-line-num new_line" data-linenumber="488" 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">

488

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<pre style="margin: 0;"> <span id="LC488" class="line" lang="d">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="481" 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">

481

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<td class="diff-line-num new_line" data-linenumber="489" 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">

489

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="d"><span class="p">}</span></span></pre>

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<td class="diff-line-num old old_line" data-linenumber="482" 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">

482

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<td class="diff-line-num new_line old" data-linenumber="490" 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="LC482" class="line" lang="d"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="483" 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">

483

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<td class="diff-line-num new_line old" data-linenumber="490" 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="LC483" class="line" lang="d"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">main</span><span class="p">()</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="484" 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">

484

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<td class="diff-line-num new_line old" data-linenumber="490" 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="LC484" class="line" lang="d"><span class="p">}</span></span></pre>

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