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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/sumalibs">Debian Med / sumalibs</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/4156e5213f8714e071f581270810ed7afc501d2b">4156e521</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T10:21:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using CMake instead of upstream's Makefile
This is to allow building a shared and a static library easily.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/f7bfe474d878398c8bd14ff5d667995051a9c9f8">f7bfe474</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T10:22:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating debian/rules to fit CMake.
Overriding dh_auto_configure to transmit arguments to CMake
Stopping overriding dh_auto_install
Putting VERSION and SOVERSION in debian/rules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/940e82888a32540fb91575484a4473459fbe3bce">940e8288</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T10:26:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Creating a shared lib and a development package
Modifying debian/control to split the package into:
* libsuma1, which provides the shared lib;
* libsuma-dev, which provides the static lib and include files.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/242357ed64e302698e748376171b743e3c164ddf">242357ed</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T10:28:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding debian/*.install files for the two binary packages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/2ca78ef582990f629b350d81f3d761ab78e29110">2ca78ef5</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T10:30:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding symbols file for the shared lib
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/4352f0a76f21752733b14cb4c8fdc37eb8b04abe">4352f0a7</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T10:31:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating debian/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/83f9e108642f446b0029831f15dfc0f158cb67cd">83f9e108</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T10:34:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding a patch to read ACGT-only sequences
Patch formerly used in the sumaclust package.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/bf90a3b1b70b3d1deb11b97d8da24b6de9b277d0">bf90a3b1</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T10:57:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing upstream's Makefile in using_cmake.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/6174a20881a47ef59d16629682de3a3670d9ae31">6174a208</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T13:27:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Overriding dh_clean to remove CMake output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/b51bac168ca8431d9dd5e7aa26c20fb6ec03f6f8">b51bac16</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T15:05:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.36</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/8c0e2ed5d72c6a1ab9b334b9441b83c47399de0a">8c0e2ed5</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T15:05:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.0.36'
Update to upstream version '1.0.36'
with Debian dir abd464a6c350129433cd0294fa6850515386c654</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/9960f0b81192c194489bf06dd78ddbeb520406a3">9960f0b8</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T15:06:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Deleting patch to read sequences, taken into account by upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/89185eacf758738aaa5a1a9433f9c796dac8db21">89185eac</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-13T18:40:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Hardening
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/01f7b4460489b4fb33d2cf409e034e45a22a7026">01f7b446</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-14T13:35:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Providing autopkgtest for building against the libs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/f44d7985bc32055b97208e4d8665d85750a3e5cb">f44d7985</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-14T15:34:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Providing autopkgtests as examples for the -dev package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/30d91520d9763b4e5fc85372d4165b1c885e7bef">30d91520</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-14T15:35:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Correcting debian/tests/run-unit-test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sumalibs/-/commit/1933b1faf6ce40fd4dea3f5bdd3b06a57569504d">1933b1fa</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-04-14T15:46:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#abaad13d61b586a210b27e7df1e70dcb2d9e227c">
<span class="new-file">
+
debian/libsuma-dev.examples
</span>
</a>
</li>
<li class="file-stats">
<a href="#7f251695fc36b4cae212d70c660623fcbc8f885a">
<span class="new-file">
+
debian/libsuma-dev.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#ce690223448ed4ffcf13fb0864a1ca6e312032b6">
<span class="new-file">
+
debian/libsuma1.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#f16964f759da9a297aef164af5c83dfaec37bfbd">
<span class="new-file">
+
debian/libsuma1.symbols
</span>
</a>
</li>
<li class="file-stats">
<a href="#ec929ef01d1cf2a9933f4a573f16144feabcf330">
<span class="deleted-file">
−
debian/patches/fix_makefile.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#1b08f8939cab89e4db504949874304f0da9e0ab4">
<span class="new-file">
+
debian/patches/using_cmake.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#6b6c8510e2a985e71be692bc0e13e709b969a016">
<span class="new-file">
+
debian/tests/buildAndSimpleRun
</span>
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
<li class="file-stats">
<a href="#051f0c14729ef6836ea177f8e34fa5512de6f6b6">
libfasta/sequence.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<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">
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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="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="k" style="font-weight: 600;">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
</pre>
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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">
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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="php"><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="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="php"></span>
</pre>
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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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<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="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sumalibs (1.0.36-1) UNRELEASED; urgency=medium</span>
</pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version 1.0.36</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Using CMake instead of upstream's Makefile</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Updating debian/rules to fit CMake.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Creating a shared lib and a development package</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Adding debian/*.install files for the two binary packages</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Adding symbols file for the shared lib</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Overriding dh_clean to remove CMake output</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Hardening compilation</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Providing autopkgtest for building against the libs</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Providing autopkgtest as an example for the -dev package</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> Tue, 14 Apr 2020 13:37:10 +0200</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">sumalibs (1.0.35-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,19 +2,34 @@ Source: sumalibs</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Pierre Gruet <pgtdebian@free.fr></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> cmake</span>
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7
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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="plaintext">Standards-Version: 4.5.0</span>
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<td class="diff-line-num 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">
8
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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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/sumalibs</span>
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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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/sumalibs.git</span>
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10
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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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: https://git.metabarcoding.org/obitools/sumalibs</span>
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<td class="diff-line-num old_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">
11
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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">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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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">
12
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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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Package: libsuma1</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Section: libs</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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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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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Description: shared library for sumatra and sumaclust</span>
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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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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Sumatra is a tool for fast and exact comparison and clustering of sequences</span>
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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="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">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> and sumaclust can be used for fast and exact clustering of genomic sequences.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Both tools are using this common library.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> .</span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext"> This package provides the shared library.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Package: libsuma-dev</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num 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">
15
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Section: libdevel</span>
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<td class="diff-line-num old old_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Description: <span class="idiff left right">libraries</span> for sumatra and sumaclust</span>
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<td class="diff-line-num new old_line" data-linenumber="18" 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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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Depends: <span class="idiff left right">libsuma1 (= ${binary:Version}), </span>${shlibs:Depends}, ${misc:Depends}</span>
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<td class="diff-line-num new old_line" data-linenumber="18" 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="30" 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">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Description: <span class="idiff left right">headers and static library</span> for sumatra and sumaclust</span>
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<td class="diff-line-num old_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">
18
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> Sumatra is a tool for fast and exact comparison and clustering of sequences</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> and sumaclust can be used for fast and exact clustering of genomic sequences.</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> Both tools are using this common library.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> This package provides the static library and header files.</span></pre>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -10,6 +10,7 @@ License: CeCILL-2</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Copyright: 2019-2020 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> 2020 Pierre Gruet <pgtdebian@free.fr></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">License: CeCILL-2</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">License: CeCILL-2</span>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#abaad13d61b586a210b27e7df1e70dcb2d9e227c"><strong>debian/libsuma-dev.examples</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/buildAndSimpleRun</span></pre>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#7f251695fc36b4cae212d70c660623fcbc8f885a"><strong>debian/libsuma-dev.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="cm" style="color: #998; font-style: italic;">/*/*.so</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="cm" style="color: #998; font-style: italic;">usr/lib/*/</span><span class="o" style="font-weight: 600;">*.</span><span class="nx">a</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#ce690223448ed4ffcf13fb0864a1ca6e312032b6"><strong>debian/libsuma1.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/*/*.</span><span class="nx">so</span><span class="o" style="font-weight: 600;">.*</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#f16964f759da9a297aef164af5c83dfaec37bfbd"><strong>debian/libsuma1.symbols</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libsuma.so.1 libsuma1 #MINVER#</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">* Build-Depends-Package: libsuma-dev</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> addCounts@Base 1.0.35</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> alignForSumathings@Base 1.0.35</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> buildTable@Base 1.0.35</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> calculateLCSmin@Base 1.0.35</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> calculateMaxAndMinLen@Base 1.0.35</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> calculateMaxAndMinLenDB@Base 1.0.35</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> calculateSSEBandLength@Base 1.0.35</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> calculateSizeToAllocate@Base 1.0.35</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> changeValue@Base 1.0.35</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> char_header_add_field@Base 1.0.35</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> check_and_realloc_field@Base 1.0.35</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> check_and_realloc_mem_in_header_table@Base 1.0.35</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> check_mem_field@Base 1.0.35</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> cleanDB@Base 1.0.35</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> compareTable@Base 1.0.35</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> end_header_table@Base 1.0.35</span>
</pre>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> errorAbort@Base 1.0.35</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> exitIfEmptyFile@Base 1.0.35</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> fastaSeqPtr_header_add_field@Base 1.0.35</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> file_nextChar@Base 1.0.35</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> file_nextLine@Base 1.0.35</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> file_open@Base 1.0.35</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> file_openrw@Base 1.0.35</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> filters@Base 1.0.35</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> filtersSumatra@Base 1.0.35</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> free_header_table@Base 1.0.35</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> generic_sse_banded_lcs_align@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> getA16Address@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> getItemFromHeader@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> hashDB@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> header_parser@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> header_parser_main@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> header_yy_create_buffer@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> header_yy_delete_buffer@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> header_yy_flex_debug@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> header_yy_flush_buffer@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> header_yy_scan_buffer@Base 1.0.35</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> header_yy_scan_bytes@Base 1.0.35</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> header_yy_scan_string@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> header_yy_switch_to_buffer@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> header_yyalloc@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> header_yyfree@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> header_yyget_debug@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> header_yyget_in@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> header_yyget_leng@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> header_yyget_lineno@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> header_yyget_out@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> header_yyget_text@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> header_yyin@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> header_yyleng@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> header_yylex_destroy@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> header_yylineno@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> header_yyout@Base 1.0.35</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> header_yypop_buffer_state@Base 1.0.35</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> header_yypush_buffer_state@Base 1.0.35</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> header_yyrealloc@Base 1.0.35</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> header_yyrestart@Base 1.0.35</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> header_yyset_debug@Base 1.0.35</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> header_yyset_in@Base 1.0.35</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> header_yyset_lineno@Base 1.0.35</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> header_yyset_out@Base 1.0.35</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> header_yytext@Base 1.0.35</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> header_yywrap@Base 1.0.35</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> iniSeq@Base 1.0.35</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> initializeAddressWithGaps@Base 1.0.35</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> int2bin@Base 1.0.35</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> isPossible@Base 1.0.35</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> isPossibleSumathings@Base 1.0.35</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> malloc_field@Base 1.0.35</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> prepareTablesForSumathings@Base 1.0.35</span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> printHeaderAndSeqFromFastaSeqPtr@Base 1.0.35</span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> printOnlyHeaderFromFastaSeqPtr@Base 1.0.35</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> printOnlyHeaderFromTable@Base 1.0.35</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> printOnlySeqFromChar@Base 1.0.35</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> printOnlySeqFromFastaSeqPtr@Base 1.0.35</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> putSeqInSeq@Base 1.0.35</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> reallocA16Address@Base 1.0.35</span>
</pre>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> realloc_field@Base 1.0.35</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> reverseSortSeqsWithCounts@Base 1.0.35</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> seq_fillDigitSeq@Base 1.0.35</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> seq_fillHeader@Base 1.0.35</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> seq_fillSeq@Base 1.0.35</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> seq_fillSeqOnlyATGC@Base 1.0.35</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> seq_findSeqByAccId@Base 1.0.35</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> seq_getNext@Base 1.0.35</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> seq_printSeqs@Base 1.0.35</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> seq_readAllSeq2@Base 1.0.35</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> seq_readNextFromFilebyLine@Base 1.0.35</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> sortSeqsWithCounts@Base 1.0.35</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> sse_banded_align_just_lcs@Base 1.0.35</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> sse_banded_align_lcs_and_ali_len@Base 1.0.35</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> sse_banded_lcs_align@Base 1.0.35</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> store_in_field@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> store_in_header_table@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> str_chopAtDelim@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> str_isSpace@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> str_removeSpaces@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> str_sepNameValue@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> str_strrstr@Base 1.0.35</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> table_header_add_field@Base 1.0.35</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> threshold4@Base 1.0.35</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> thresholdLCS4@Base 1.0.35</span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> uniqSeqsVector@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> util_findInArr@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> util_free@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> util_malloc@Base 1.0.35</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> util_realloc@Base 1.0.35</span></pre>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#ec929ef01d1cf2a9933f4a573f16144feabcf330"><strong>debian/patches/fix_makefile.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 09 Jul 2019 15:59:36 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Do not force PREFIX to /usr/local</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- a/Makefile</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PREFIX=/usr/local</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PREFIX=/usr</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> SOURCES = libfasta/fasta_header_parser.c \</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> libfasta/fasta_seq_writer.c \</span></pre>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">fix_makefil</span>e.patch</span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">using_cmak</span>e.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#1b08f8939cab89e4db504949874304f0da9e0ab4"><strong>debian/patches/using_cmake.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Using CMake instead of original Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Upstream provides a Makefile. In order to build both a shared and a static </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> library, we use a construction with CMake.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2020-04-13</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- /dev/null</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;">+++ b/CMakeLists.txt</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -0,0 +1,63 @@</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+cmake_minimum_required(VERSION 3.16)</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+project(sumalibs)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(CMAKE_INSTALL_PREFIX "/usr")</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+include_directories(include)</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+file(GLOB_RECURSE</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ lib_files</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libfasta/*.c</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libfile/fileHandling.c</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ liblcs/sse_banded_LCS_alignment.c</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ liblcs/upperband.c</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libutils/*.c</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+)</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+add_library(suma</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SHARED</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${lib_files}</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+)</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+target_include_directories(suma PUBLIC</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libfasta/</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libfile/</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ liblcs/</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libutils/</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libsse/</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+)</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set_target_properties(suma PROPERTIES</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ VERSION ${VERSION}</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SOVERSION ${SOVERSION}</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+)</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+add_library(sumaa</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ STATIC</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${lib_files}</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+)</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+target_include_directories(sumaa PUBLIC</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libfasta/</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libfile/</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ liblcs/</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libutils/</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libsse/</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set_target_properties(sumaa PROPERTIES</span></span>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ OUTPUT_NAME suma</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -w -g")</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+install(TARGETS suma DESTINATION "lib/${CMAKE_LIBRARY_ARCHITECTURE}")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+install(TARGETS sumaa DESTINATION "lib/${CMAKE_LIBRARY_ARCHITECTURE}")</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+install(DIRECTORY</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libfasta</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libfile</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ liblcs</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libutils</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libsse</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DESTINATION include</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ FILES_MATCHING PATTERN "*.h")</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ /dev/null</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="p">@@ -1,56 +0,0 @@</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PREFIX=/usr/local</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SOURCES = libfasta/fasta_header_parser.c \</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- libfasta/fasta_seq_writer.c \</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- libfasta/fasta_header_handler.c \</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- libfasta/header_mem_handler.c \</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- libfasta/sequence.c \</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- libfile/fileHandling.c \</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- liblcs/sse_banded_LCS_alignment.c \</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- liblcs/upperband.c \</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- libutils/utilities.c \</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- libutils/debug.c </span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SRCS=$(SOURCES)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-OBJECTS= $(patsubst %.c,%.o,$(SOURCES))</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LIBFILE = libsuma.a</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-RANLIB = ranlib</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CC=gcc</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LDFLAGS=</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = -O3 -w</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-default: all</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all: $(LIBFILE)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-%.o: %.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) -c -o $@ $< $(LIB)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-libfasta/fasta_header_parser.c: libfasta/fasta_header_parser.l</span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- flex -Pheader_yy -t $< > $@</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-libfasta/dic_parser.c: libfasta/dic_parser.l</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lex -Phashtable_yy -t $< > $@</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-clean:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -rf $(OBJECTS) $(LIBFILE)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$(LIBFILE): $(OBJECTS)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="120" 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">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ar -cr $@ $?</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" 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">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(RANLIB) $@</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="123" 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">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-install: all</span></span>
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<td class="diff-line-num new new_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install -d $(DESTDIR)$(PREFIX)/lib/</span></span>
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install -m 644 $(LIBFILE) $(DESTDIR)$(PREFIX)/lib/</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install -d $(DESTDIR)$(PREFIX)/include/</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for lib in libfasta liblcs libsse libutils libfile ; do \</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install -d $(DESTDIR)$(PREFIX)/include/$$lib ; \</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cp $$lib/*.h $(DESTDIR)$(PREFIX)/include/$$lib ; \</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- done</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -5,10 +5,31 @@ export LC_ALL=C.UTF-8</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">DPKG_EXPORT_BUILDFLAGS = 1</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">include /usr/share/dpkg/buildflags.mk</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">CFLAGS+=$(CPPFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">CXXFLAGS+=$(CPPFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">#Set VERSION and SOVERSION</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">VERSION=1.0</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">SOVERSION=1</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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8
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">%:</span>
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9
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> dh $@</span>
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10
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">override_dh_install:</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> dh_install</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> mkdir debian/libsuma-dev/usr/lib/$(DEB_HOST_MULTIARCH)</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> mv debian/libsuma-dev/usr/lib/*.a debian/libsuma-dev/usr/lib/$(DEB_HOST_MULTIARCH)</span></pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">override_dh_auto_configure:</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> dh_auto_configure -- \</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> -DCMAKE_LIBRARY_ARCHITECTURE="$(DEB_HOST_MULTIARCH)" \</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> -DVERSION="$(VERSION)" \</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> -DSOVERSION="$(SOVERSION)"</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">override_dh_clean:</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> dh_clean</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> -rm -rf $(CURDIR)/debian/tmp</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> -rm -rf $(CURDIR)/debian/libsuma1</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> -rm -rf $(CURDIR)/debian/libsuma-dev</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> -rm -rf $(CURDIR)/debian/*debhelper*</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> -rm $(CURDIR)/debian/*.substvars</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> -rm $(CURDIR)/debian/files</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> -rm -rf $(CURDIR)/obj-$(DEB_HOST_MULTIARCH)</span></pre>
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<li id="6b6c8510e2a985e71be692bc0e13e709b969a016">
<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#6b6c8510e2a985e71be692bc0e13e709b969a016"><strong>debian/tests/buildAndSimpleRun</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># autopkgtest check: build and run a program against sumalibs. We check that </span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># it builds and that it behaves well on a very simple reading exercise.</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># (C) 2020 Pierre Gruet.</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">WORKDIR</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span><span class="si" style="color: #d14;">)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$WORKDIR</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$WORKDIR</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> > test.fasta</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ1</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="sh" style="color: #d14;">ACGATCGCACGCATCGTCAG</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="sh" style="color: #d14;">>SEQ2</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="sh" style="color: #d14;">ACGTAGCTAGCA</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> > main.c</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="sh" style="color: #d14;">#include <stdio.h></span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="sh" style="color: #d14;">#include <libfasta/sequence.h></span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="sh" style="color: #d14;">int main()</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">{</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;"> fastaSeqCount n;</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;"> n=seq_readAllSeq2("test.fasta", 1, 1);</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="sh" style="color: #d14;"> printf("%d sequences are read</span><span class="se" style="color: #d14;">\n</span><span class="sh" style="color: #d14;">", n.count);</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="sh" style="color: #d14;"> </span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="sh" style="color: #d14;"> return 0;</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="sh" style="color: #d14;">}</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">gcc <span class="nt" style="color: #000080;">-c</span> <span class="nt" style="color: #000080;">-o</span> main.o main.c</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell">gcc <span class="nt" style="color: #000080;">-o</span> testPrg main.o <span class="nt" style="color: #000080;">-lsuma</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build done"</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-x</span> testPrg <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"> ./testPrg |</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-n</span> <span class="s1" style="color: #d14;">'s/.sequences.*//p'</span> |</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"2"</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> </span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: buildAndSimpleRun</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, build-essential</span></pre>
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<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>libsuma-dev</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">sh buildAndSimpleRun</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test buildAndSimpleRun PASSED"</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test buildAndSimpleRun FAILED"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span></pre>
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<li id="051f0c14729ef6836ea177f8e34fa5512de6f6b6">
<a href="https://salsa.debian.org/med-team/sumalibs/-/compare/ea09ec9fd34e7a8a5debcdc146a57fad822647ca...1933b1faf6ce40fd4dea3f5bdd3b06a57569504d#051f0c14729ef6836ea177f8e34fa5512de6f6b6"><strong>libfasta/sequence.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="162" style="width: 35px; color: rgba(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="162" style="width: 35px; color: rgba(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">@@ -162,19 +162,24 @@ void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem, int seqLen)</td>
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162
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c"><span class="p">{</span></span>
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seqTemp</span><span class="p">;</span></span>
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">,</span> <span class="n" style="color: #333;">seqIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">,</span> <span class="n" style="color: #333;">seqIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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166
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seqAlphabets</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"acgtACGT"</span><span class="p">;</span></span>
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167
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">notAllATGC</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">goOnParsing</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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168
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"></span>
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169
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">seqTemp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">util_malloc</span><span class="p">(</span><span class="n" style="color: #333;">seqLen</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">),</span> <span class="n" style="color: #333;">__FILE__</span><span class="p">,</span> <span class="n" style="color: #333;">__LINE__</span><span class="p">);</span></span>
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170
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">index</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">len</span></span><span class="p">)</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">goOnParsing</span></span><span class="p">)</span></span>
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172
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"> <span class="p">{</span></span>
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173
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>
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174
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;">seqAlphabets</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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175
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">seqTemp</span><span class="p">[</span><span class="n" style="color: #333;">seqIndex</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tolower</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'\0'</span><span class="p">)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">goOnParsing</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// end of the sequence has been reached.</span></span>
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176
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span></span>
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177
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">notAllATGC</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">goOnParsing</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="c"> <span class="p">}</span></span>
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179
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c"></span>
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180
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">notAllATGC</span><span class="p">)</span></span>
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