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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/plast">Debian Med / plast</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plast/-/commit/53a572d410d1781e361a50bc991e7953c6077913">53a572d4</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-01-24T23:36:42+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop d/p/use_debian_packaged_pcre.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plast/-/commit/960a9557465c5b7c9e804d7ca0663cdc14202399">960a9557</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-01-24T23:38:07+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add pcre.patch to build with pcre2 (Closes: #999991)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plast/-/commit/c8d0bacc015d0a4eb73ebf5f7b23403cd6cd8e90">c8d0bacc</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-01-24T23:38:15+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: B-D on libpcre2-dev instead of libpcre3-dev
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plast/-/commit/0b9d88cfa9e01a1cd09a723a22d91387317696fe">0b9d88cf</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-01-24T23:44:41+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Dep3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plast/-/commit/a0c9991372044cd5557f55e6bfbbf65532aeee48">a0c99913</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-01-24T23:45:35+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#be0cf27adb42327fb530edfc5771fbcb56dfaff5">
<span class="new-file">
+
debian/patches/pcre.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#3b31e5b19608cc1fdb42cb6915c5e2a89dec9858">
<span class="deleted-file">
−
debian/patches/use_debian_packaged_pcre.patch
</span>
</a>
</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plast/-/compare/6100467a418b032b7e588a0060c76c9775cae9aa...a0c9991372044cd5557f55e6bfbbf65532aeee48#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plast (2.3.2+dfsg-8) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Drop d/p/use_debian_packaged_pcre.patch</span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add pcre.patch to build with pcre2 (Closes: #999991)</span>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * d/control: B-D on libpcre2-dev instead of libpcre3-dev</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"> -- Nilesh Patra <nilesh@debian.org> Mon, 24 Jan 2022 23:44:55 +0530</span>
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<td class="new_line diff-line-num new" data-linenumber="9" 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="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">plast (2.3.2+dfsg-7) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/plast/-/compare/6100467a418b032b7e588a0060c76c9775cae9aa...a0c9991372044cd5557f55e6bfbbf65532aeee48#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">@@ -5,7 +5,7 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> libpcre<span class="idiff left right">3</span>-dev,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> libpcre<span class="idiff left right">2</span>-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> default-jdk,</span>
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libsimde-dev</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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<a href="https://salsa.debian.org/med-team/plast/-/compare/6100467a418b032b7e588a0060c76c9775cae9aa...a0c9991372044cd5557f55e6bfbbf65532aeee48#be0cf27adb42327fb530edfc5771fbcb56dfaff5"><strong>debian/patches/pcre.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Port code to pcre2</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/PLAST-software/plast-library/issues/10</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Jan 24, 2022</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/alignment/filter/impl/AlignmentFilterOperator.cpp</span></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/src/alignment/filter/impl/AlignmentFilterOperator.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -156,19 +156,16 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ** REMARKS :</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> *********************************************************************/</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> AlignmentFilterRegexOperator::AlignmentFilterRegexOperator (const std::vector<std::string>& args)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- : AlignmentFilterUnaryOperator<std::string>(args), _reg(0), _regExtra(0)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ : AlignmentFilterUnaryOperator<std::string>(args), _reg(0)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- const char* pcreErrorStr = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int pcreErrorOffset = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int pcreErrorStr = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PCRE2_SIZE pcreErrorOffset = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> /** We compile the regexp. */</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- _reg = pcre_compile (_value.c_str(), 0, &pcreErrorStr, &pcreErrorOffset, NULL);</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ _reg = pcre2_compile ((PCRE2_SPTR)_value.c_str(), PCRE2_ZERO_TERMINATED, 0, &pcreErrorStr, &pcreErrorOffset, NULL);</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- /** We optimize the regex. */</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (_reg != 0) { _regExtra = pcre_study (_reg, 0, &pcreErrorStr); }</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DEBUG (("AlignmentFilterRegexOperator::AlignmentFilterRegexOperator _value='%s' _reg=%p _regExtra=%p\n",</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- _value.c_str(), _reg, _regExtra</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DEBUG (("AlignmentFilterRegexOperator::AlignmentFilterRegexOperator _value='%s' _reg=%p\n",</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;">+ _value.c_str(), _reg</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> ));</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -182,8 +179,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> *********************************************************************/</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> AlignmentFilterRegexOperator::~AlignmentFilterRegexOperator ()</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (_reg) { pcre_free (_reg); }</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (_regExtra) { pcre_free (_regExtra); }</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (_reg) { pcre2_code_free (_reg); }</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> DEBUG (("AlignmentFilterRegexOperator::~AlignmentFilterRegexOperator\n"));</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/alignment/filter/impl/AlignmentFilterOperator.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/alignment/filter/impl/AlignmentFilterOperator.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -28,7 +28,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> #include <alignment/filter/api/IAlignmentFilter.hpp></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> #include <designpattern/impl/Property.hpp></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> #include <stdarg.h></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <pcre/pcre.h></span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define PCRE2_CODE_UNIT_WIDTH 8</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <pcre2.h></span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> /********************************************************************************/</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> namespace alignment {</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -196,14 +197,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> /** */</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> AlignmentFilterRegexOperator (const std::vector<std::string>& args);</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AlignmentFilterRegexOperator () : AlignmentFilterUnaryOperator<std::string>(), _reg(0), _regExtra(0) {}</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AlignmentFilterRegexOperator () : AlignmentFilterUnaryOperator<std::string>(), _reg(0) {}</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> ~AlignmentFilterRegexOperator ();</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> protected:</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pcre* _reg;</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pcre_extra* _regExtra;</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pcre2_code *_reg;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> /********************************************************************************/</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -248,10 +247,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> bool isOk (const core::Alignment& a) const { \</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> if (_reg==0) { return false; } \</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> std::string tmp(regexp); /* Not optimal but we may call with const char* or std::string. */ \</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pcre2_match_data *match_data = pcre2_match_data_create_from_pattern(_reg, NULL); \</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> switch(_operator) \</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> { \</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- case HOLD: return pcre_exec (_reg, _regExtra, tmp.c_str(), tmp.size(), 0, 0, NULL, 0) >= 0; \</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;">- case NO_HOLD: return pcre_exec (_reg, _regExtra, tmp.c_str(), tmp.size(), 0, 0, NULL, 0) < 0; \</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case HOLD: return pcre2_match (_reg, (PCRE2_SPTR)tmp.c_str(), tmp.size(), 0, 0, match_data, NULL) >= 0; \</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ case NO_HOLD: return pcre2_match (_reg, (PCRE2_SPTR)tmp.c_str(), tmp.size(), 0, 0, match_data, NULL) < 0; \</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> default: return false; \</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> } \</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> } \</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="p">@@ -46,7 +46,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> include_directories (${PROJECT_BINARY_DIR}/include ${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2})</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> add_library (PlastLibrary SHARED ${PlastLibraryFiles} )</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> add_executable (plast ${PlastCmdFiles})</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;">-target_link_libraries (plast pthread)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+target_link_libraries (plast pthread -lpcre2-8)</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> ################################################################################</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> # OS specific stuffs</span></pre>
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<a href="https://salsa.debian.org/med-team/plast/-/compare/6100467a418b032b7e588a0060c76c9775cae9aa...a0c9991372044cd5557f55e6bfbbf65532aeee48#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">use_debian_packaged_pcre.patch</span>
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2
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">adapt_auto_test_script.sh</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">no_msse3.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">reproducible.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">simde.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">pcre.patch</span></pre>
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<li id="3b31e5b19608cc1fdb42cb6915c5e2a89dec9858">
<a href="https://salsa.debian.org/med-team/plast/-/compare/6100467a418b032b7e588a0060c76c9775cae9aa...a0c9991372044cd5557f55e6bfbbf65532aeee48#3b31e5b19608cc1fdb42cb6915c5e2a89dec9858"><strong>debian/patches/use_debian_packaged_pcre.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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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 09 Feb 2016 10:20:36 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Use Debian packaged pcre lib instead of internal code copy</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/src/alignment/filter/impl/AlignmentFilterOperator.hpp</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/src/alignment/filter/impl/AlignmentFilterOperator.hpp</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -28,7 +28,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> #include <alignment/filter/api/IAlignmentFilter.hpp></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> #include <designpattern/impl/Property.hpp></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> #include <stdarg.h></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <pcre/pcre.h></span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <pcre.h></span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> /********************************************************************************/</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> namespace alignment {</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -44,7 +44,7 @@</span> add_definitions (-O3 -funroll-loop</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> include_directories (${PROJECT_BINARY_DIR}/include ${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2})</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> add_library (PlastLibrary SHARED ${PlastLibraryFiles} )</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> add_executable (plast ${PlastCmdFiles})</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-target_link_libraries (plast pthread)</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+target_link_libraries (plast pthread pcre)</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> # OS specific stuffs</span></pre>
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