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<h3>
Antoni Villalonga pushed to branch master
at <a href="https://salsa.debian.org/med-team/vt">Debian Med / vt</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vt/-/commit/5ec43202af6323f61ae4e179536f3fd877d4ff0f">5ec43202</a></strong>
<div>
<span>by Antoni Villalonga</span>
<i>at 2020-06-17T10:31:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control Add missing dependency on r-base-core
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vt/-/commit/950e7d4cdea98ceae27ce8d49432b3f56b4fb8b9">950e7d4c</a></strong>
<div>
<span>by Antoni Villalonga</span>
<i>at 2020-06-17T11:04:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Makefile use env CXXFLAGS to pass blhc tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vt/-/commit/5fbf3eeb699a483edcdc18a3b77e5d6066ad5c56">5fbf3eeb</a></strong>
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<span>by Antoni Villalonga</span>
<i>at 2020-06-18T09:12:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapted to recent versions of external libs and warn on test errors
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/vt/-/commit/767b74bceabe6672ed178e999721e5c1186a63da">767b74bc</a></strong>
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<span>by Antoni Villalonga</span>
<i>at 2020-06-18T09:16:23+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#cd4e4b7398e1f7fade391419850269be91c9dd2d">
debian/patches/makefile
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#e6f85e90d2a0e38f5db109442fb0c105003a2745">
<span class="new-file">
+
debian/patches/test-fail-on-error
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/vt/-/compare/489a79eb6389c9abc44aa26e829dfc53b5102392...767b74bceabe6672ed178e999721e5c1186a63da#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">vt (0.57721-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * d/control Add missing dependency on r-base-core</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Makefile use env CXXFLAGS to pass blhc tests</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Adapted to recent versions of external libs and warn on test errors</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Antoni Villalonga <antoni@friki.cat> Thu, 18 Jun 2020 09:12:40 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">vt (0.57721-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Initial release</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/vt/-/compare/489a79eb6389c9abc44aa26e829dfc53b5102392...767b74bceabe6672ed178e999721e5c1186a63da#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,7 +23,9 @@ Rules-Requires-Root: no</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Package: vt</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num old old_line" data-linenumber="26" 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="26" 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="LC26" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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<td class="diff-line-num new old_line" data-linenumber="27" 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="LC26" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> ${misc:Depends},</span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> r-base-core,</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Description: Tool set for short variant discovery in genetic sequence data</span>
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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">
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> vt is a variant tool set that discovers short variants from Next Generation</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> Sequencing data.</span>
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<a href="https://salsa.debian.org/med-team/vt/-/compare/489a79eb6389c9abc44aa26e829dfc53b5102392...767b74bceabe6672ed178e999721e5c1186a63da#cd4e4b7398e1f7fade391419850269be91c9dd2d"><strong>debian/patches/makefile</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="nl">Description</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Build again external/system libs</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="make"><span class="idiff left"> Remove </span><span class="nb" style="color: #0086b3;"><span class="idiff">local </span></span><span class="idiff right">lib</span>s</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="idiff left"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">Migration</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">from</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">1.8</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">to</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">1.10</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">libht</span>s</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="nl">Author</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Antoni Villalonga i Noceras <antoni@friki.cat></span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="make"><span class="nl">Last-Update</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Wed</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;"> 1<span class="idiff left right">7 Jun 2020 03:31:27</span> +0200</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="make"><span class="nl">Last-Update</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Wed</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;"> 1<span class="idiff left right">8 Jun 2020 09:10:04</span> +0200</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">---</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">a/Makefile</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+++</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">b/Makefile</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-1,6</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+1,<span class="idiff left right">7</span></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-1,6</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+1,<span class="idiff left right">6</span></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"> <span class="nv" style="color: #008080;">OPTFLAG</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-O3</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">-INCLUDES</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-I</span>./lib <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-I</span>./lib/htslib <span class="nt" style="color: #000080;">-I</span>./lib/Rmath <span class="nt" style="color: #000080;">-I</span>./lib/pcre2</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">-CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-pipe</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++0x <span class="nv" style="color: #008080;">$(OPTFLAG)</span> <span class="nv" style="color: #008080;">$(INCLUDES)</span> <span class="nt" style="color: #000080;">-D__STDC_LIMIT_MACROS</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span><span class="nv" style="color: #008080;">INCLUDES</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-I</span>/usr/share/R/include</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">$(CXXFLAGS)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-pipe</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++0x <span class="nv" style="color: #008080;">$(OPTFLAG)</span> <span class="nv" style="color: #008080;">$(INCLUDES)</span> <span class="nt" style="color: #000080;">-D__STDC_LIMIT_MACROS</span> <span class="nt" style="color: #000080;">-DPCRE2_CODE_UNIT_WIDTH</span><span class="o" style="font-weight: 600;">=</span>8</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-pipe</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++0x <span class="nv" style="color: #008080;">$(OPTFLAG)</span> <span class="nv" style="color: #008080;">$(INCLUDES)</span> <span class="nt" style="color: #000080;">-D__STDC_LIMIT_MACROS</span> <span class="nt" style="color: #000080;">-DPCRE2_CODE_UNIT_WIDTH</span><span class="o" style="font-weight: 600;">=</span>8</span>
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14
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"> <span class="nv" style="color: #008080;">CXX</span> <span class="o" style="font-weight: 600;">=</span> g++</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"> </span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"> <span class="nv" style="color: #008080;">SOURCESONLY</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-139,52</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+1<span class="idiff left right">40</span>,26</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-139,52</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+1<span class="idiff left right">39</span>,26</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"> <span class="nv" style="color: #008080;">TARGET</span> <span class="o" style="font-weight: 600;">=</span> vt</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"> <span class="nv" style="color: #008080;">TOOLSRC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(SOURCES:=.cpp)</span> <span class="nv" style="color: #008080;">$(SOURCESONLY)</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"> <span class="nv" style="color: #008080;">TOOLOBJ</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(TOOLSRC:.cpp=.o)</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">@@ -86,7 +85,7 @@ Last-Update: Wed, 17 Jun 2020 03:31:27 +0200</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">if</span> <span class="nv" style="color: #008080;">(i</span><span class="o" style="font-weight: 600;">==</span>buffer.end<span class="o" style="font-weight: 600;">())</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="make"><span class="nl">- int32_t cutoff_pos1 = std</span><span class="o" style="font-weight: 600;">::</span><span class="nf" style="color: #900; font-weight: 600;">max(bcf_get_pos1(buffer.front())-window</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">1);</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="make"><span class="nl">+ int32_t cutoff_pos1 = std</span><span class="o" style="font-weight: 600;">::</span><span class="nf" style="color: #900; font-weight: 600;">max((int)bcf_get_pos1(buffer.front())-window</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">1);</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="make"><span class="nl">+ int32_t cutoff_pos1 = std</span><span class="o" style="font-weight: 600;">::</span><span class="nf" style="color: #900; font-weight: 600;">max((int<span class="idiff left right">32_t</span>)bcf_get_pos1(buffer.front())-window</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">1);</span></span>
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90
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">if</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(bcf_get_pos1(v)<cutoff_pos1)</span></span>
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91
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="make"> <span class="nl">fprintf(stderr, "[%s</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d)</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;"> please increase window size to at least %d.</span>\n<span class="nf" style="color: #900; font-weight: 600;">"</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,7 +94,7 @@ Last-Update: Wed, 17 Jun 2020 03:31:27 +0200</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">if</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(buffer.size()>1)</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="make"><span class="nl">- int32_t cutoff_pos1 = std</span><span class="o" style="font-weight: 600;">::</span><span class="nf" style="color: #900; font-weight: 600;">max(bcf_get_pos1(buffer.front())-window</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">1);</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="make"><span class="nl">+ int32_t cutoff_pos1 = std</span><span class="o" style="font-weight: 600;">::</span><span class="nf" style="color: #900; font-weight: 600;">max((int)bcf_get_pos1(buffer.front())-window</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">1);</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="make"><span class="nl">+ int32_t cutoff_pos1 = std</span><span class="o" style="font-weight: 600;">::</span><span class="nf" style="color: #900; font-weight: 600;">max((int<span class="idiff left right">32_t</span>)bcf_get_pos1(buffer.front())-window</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">1);</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="make"> </span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">while</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(buffer.size()>1)</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</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">@@ -233,3 +232,25 @@ Last-Update: Wed, 17 Jun 2020 03:31:27 +0200</td>
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233
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;">#include "candidate_region_extractor.h"</span></span>
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234
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;">#include "candidate_motif_picker.h"</span></span>
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235
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;">#include "flank_detector.h"</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">---</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">a/hts_utils.h</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+++</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">b/hts_utils.h</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-40,9</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+40,11</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">*FAI</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">UTILS</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">**********/</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">typedef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">struct</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="241" 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">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">int</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">id;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">//</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">faidx_t->name[id]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">is</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">for</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">this</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">struct.</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">int32_t</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">line_len,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">line_blen;</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">int64_t</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">len;</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">uint64_t</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">offset;</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">uint64_t</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">qual_offset;</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">faidx1_t;</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="make"> </span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">KHASH_MAP_INIT_STR(s,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">faidx1_t)</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-52,6</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+54,7</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@@</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">int</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">n,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">m;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="251" 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">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">char</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">**name;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">khash_t(s)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">*hash;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">enum</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">fai_format_options</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">format;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="254" 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">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">};</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="make"> </span>
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<td class="diff-line-num new new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">/**</span></span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/vt/-/compare/489a79eb6389c9abc44aa26e829dfc53b5102392...767b74bceabe6672ed178e999721e5c1186a63da#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">makefile</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix-spelling</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">test-fail-on-error</span></pre>
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<a href="https://salsa.debian.org/med-team/vt/-/compare/489a79eb6389c9abc44aa26e829dfc53b5102392...767b74bceabe6672ed178e999721e5c1186a63da#e6f85e90d2a0e38f5db109442fb0c105003a2745"><strong>debian/patches/test-fail-on-error</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test.sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test.sh</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -235,3 +235,5 @@</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> echo -n ${PASSED_TESTS} </span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> echo -n " / "</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> echo ${NO_TESTS} </span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+[ ${PASSED_TESTS} -eq ${NO_TESTS} ]</span></span></pre>
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