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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/ksw2">Debian Med / ksw2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ksw2/-/commit/20187b1340e84f5ddaa246ae0669828fa76990d0">20187b13</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-15T08:21:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup templates, add watch file, enhance citation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ksw2/-/commit/7d54606e06efa26d6b27e3e94a0095e0c3f79008">7d54606e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-15T08:21:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.0+git20190429.f06f9b3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ksw2/-/commit/3ba79079b95574652f59ec5d96d06b5bd3e06cd2">3ba79079</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-15T08:21:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.0+git20190429.f06f9b3'
Update to upstream version '0.0+git20190429.f06f9b3'
with Debian dir 69f2a84ea32462efae656dd1ba5b475284897616</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ksw2/-/commit/a9a9314719cef483cb8eb5126c6a17776377e523">a9a93147</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-15T09:53:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use autoconf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ksw2/-/commit/283fc286a1f27a345cecd9f31e5201e12f6716b4">283fc286</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-15T11:05:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use autoconf to get a proper library package
</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
<span class="new-file">
+
.gitignore
</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="#397e0622e96d3c7b30354a088612a150afa03ccc">
<span class="deleted-file">
−
debian/libksw2-0.triggers
</span>
</a>
</li>
<li class="file-stats">
<a href="#7ff75c410dc712f76b983b558527a7cf3e674e71">
<span class="deleted-file">
−
debian/libksw2-dev.dirs
</span>
</a>
</li>
<li class="file-stats">
<a href="#f6361e25b2927c77444e8b661a216d7f56f9d1f8">
<span class="deleted-file">
−
debian/patches/Makefile.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#6d5507768ac8975f221ead23baef90cb894ce802">
<span class="new-file">
+
debian/patches/autoconf.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#38a607d3983d0c698515dc04da7498f38de6df4d">
<span class="deleted-file">
−
debian/postinst
</span>
</a>
</li>
<li class="file-stats">
<a href="#4466ea135ee9e99902dde6a042ccca599e084c1d">
<span class="deleted-file">
−
debian/postrm
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#a66dc2ea3b71d53e879ee60efe57194450fd06cb">
<span class="deleted-file">
−
debian/salsa-ci.yml.ex
</span>
</a>
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<li class="file-stats">
<a href="#b8e122337dd307496078a30b70e46e5cf5c64f4b">
<span class="deleted-file">
−
debian/shlibs.local.ex
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<span class="new-file">
+
debian/watch
</span>
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</li>
<li class="file-stats">
<a href="#5d1f13dff4d26c5c7b8078725799f70441eb6bef">
<span class="deleted-file">
−
debian/watch.ex
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.*.swp</span>
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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">*.dSYM</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">*.a</span>
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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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">*.o</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ksw2 (0.0+<span class="idiff left right">20190429+gitf06f9b3-1) unstable</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ksw2 (0.0+<span class="idiff left right">git20190429.f06f9b3-1) UNRELEASED</span>; urgency=medium</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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"> * Initial release (Closes: #nnnn)<span class="idiff left right"> <nnnn is the bug number of your ITP></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #nnnn)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Thu, 14 May 2020 20:48:41 +0200</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,10 @@ Source: ksw2</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC3" 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="LC4" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;">-<span id="LC5" 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">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> autoconf-archive,</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> pkg-config,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> zlib1g-dev</span>
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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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Section: libs</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Homepage: https://github.com/lh3/ksw2</span>
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<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#397e0622e96d3c7b30354a088612a150afa03ccc"><strong>debian/libksw2-0.triggers</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">activate-noawait ldconfig</span></pre>
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<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#7ff75c410dc712f76b983b558527a7cf3e674e71"><strong>debian/libksw2-dev.dirs</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/include/ksw2</span></pre>
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<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#f6361e25b2927c77444e8b661a216d7f56f9d1f8"><strong>debian/patches/Makefile.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ksw2-0.0+20200514+gitf06f9b3/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ksw2-0.0+20200514+gitf06f9b3.orig/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ksw2-0.0+20200514+gitf06f9b3/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -1,5 +1,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CC= gcc</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS= -g -Wall -Wextra -Wc++-compat -O2</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CC ?= gcc</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;">+CFLAGS ?= -g -Wall -Wextra -O2</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAG += -Wc++-compat</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS += -fPIC</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> CPPFLAGS= -DHAVE_KALLOC</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> INCLUDES= -I.</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> OBJS= ksw2_gg.o ksw2_gg2.o ksw2_gg2_sse.o ksw2_extz.o ksw2_extz2_sse.o \</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="p">@@ -33,7 +35,10 @@</span> endif</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> .c.o:</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all:$(PROG)</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+all:$(PROG) library</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;">+</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+library: $(OBJS) kalloc.o</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;">+ $(CC) -shared -o libksw2.so.0.0.20190429 -Wl,-soname,libksw2.so.0 $(OBJS) kalloc.o</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"> ksw2-test:cli.o kalloc.o $(OBJS)</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> $(CC) $(CFLAGS) $^ -o $@ $(LIBS_MORE) $(LIBS)</span></pre>
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<li id="6d5507768ac8975f221ead23baef90cb894ce802">
<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#6d5507768ac8975f221ead23baef90cb894ce802"><strong>debian/patches/autoconf.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -0,0 +1,19 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lib_LTLIBRARIES = libksw2.la</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libksw2dir=$(includedir)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libksw2_HEADERS=kalloc.h kseq.h ksw2.h</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libksw2_la_SOURCES = ksw2_gg.c ksw2_gg2.c ksw2_gg2_sse.c ksw2_extz.c ksw2_extz2_sse.c \</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ksw2_extd.c ksw2_extd2_sse.c ksw2_extf2_sse.c ksw2_exts2_sse.c \</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;">+ kalloc.c</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;">+libksw2_la_LDFLAGS = -version-info @LIB_VERSION@</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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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libksw2_la_CPPFLAGS = $(INCLUDES)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bin_PROGRAMS = ksw2-test</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ksw2_test_SOURCES = cli.c</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ksw2_test_LDADD = libksw2.la</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+pkgconfigdir=$(libdir)/pkgconfig</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;">+pkgconfig_DATA = libksw2.pc</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;">+</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;">+</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</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;">+++ b/configure.ac</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -0,0 +1,68 @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# -*- Autoconf -*-</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Process this file with autoconf to produce a configure script.</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;">+</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;">+AC_INIT(ksw2, 0.0, lh3@me.com)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CONFIG_HEADERS([config.h])</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+dnl AC_CONFIG_MACRO_DIR([/usr/share/aclocal]) - this does not help to find ax_check_zlib.m4</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;">+</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;">+AC_PREREQ(2.57)</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;">+</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;">+# Directory that contains install-sh and other auxiliary files</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;">+AC_CONFIG_AUX_DIR([config])</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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<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;">+# According to (http://www.mail-archive.com/autoconf@gnu.org/msg14232.html)</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;">+# this macro should be after AC_INIT but before AM_INIT_AUTOMAKE</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;">+################################################################################</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;">+AC_CONFIG_MACRO_DIR(config)</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;">+AM_INIT_AUTOMAKE([1.6 foreign dist-zip tar-ustar filename-length-max=299])</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;">+</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_VERSION=0:0</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;">+AC_SUBST([VERSION])</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;">+AC_SUBST([LIB_VERSION])</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;">+</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;">+AC_SUBST([VERSION])</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;">+</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;">+# Checks for programs.</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;">+AC_PROG_LN_S</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;">+AC_PROG_INSTALL</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;">+AC_PROG_LIBTOOL</span></span>
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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;">+</span></span>
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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;">+################################################################################</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;">+# calling AC_PROG_CXX resets CXXFLAGS, we use our own flags set in the</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;">+# the AX_CXXFLAGS macro below.</span></span>
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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;">+# So we cache the argument to configure</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;">+# here in ARG_CXX_FLAGS (so that our macro does not override them)</span></span>
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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;">+################################################################################</span></span>
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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;">+ARG_CXX_FLAGS="$CXXFLAGS"</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_PROG_CXX</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Ranlib handled by check for libtool</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CXXFLAGS="$ARG_CXX_FLAGS"</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;">+dnl AX_CXXFLAGS</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;">+</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;">+AC_SUBST(CXXFLAGS)</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;">+</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS="-I\$(top_srcdir) $CPPFLAGS"</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;">+# Checks for libraries.</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+m4_include([ax_check_zlib.m4])</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AX_CHECK_ZLIB()</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Checks for header files.</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_HEADER_STDC</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CHECK_HEADERS([stdlib.h])</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_PROG_MAKE_SET</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_DEFINE([HAVE_KALLOC], [], [Use ksw2's own malloc functions])</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</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;">+AC_CONFIG_FILES([</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Makefile</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libksw2.pc</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ])</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_OUTPUT</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</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;">+</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;">--- /dev/null</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libksw2.pc.in</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="p">@@ -0,0 +1,12 @@</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+prefix=@prefix@</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+exec_prefix=${prefix}</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libdir=${exec_prefix}/lib</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+includedir=${prefix}/include</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Name: libksw</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Version: @VERSION@</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Description: globl alignment and alignment extension library</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Libs: -L${libdir} -lksw2</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Cflags: -I${includedir}</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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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;">--- a/Makefile</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ /dev/null</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="p">@@ -1,58 +0,0 @@</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;">-CC= gcc</span></span>
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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;">-CFLAGS= -g -Wall -Wextra -Wc++-compat -O2</span></span>
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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;">-CPPFLAGS= -DHAVE_KALLOC</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;">-INCLUDES= -I.</span></span>
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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;">-OBJS= ksw2_gg.o ksw2_gg2.o ksw2_gg2_sse.o ksw2_extz.o ksw2_extz2_sse.o \</span></span>
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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;">- ksw2_extd.o ksw2_extd2_sse.o ksw2_extf2_sse.o ksw2_exts2_sse.o</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;">-PROG= ksw2-test</span></span>
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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;">-LIBS= -lz</span></span>
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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;">-</span></span>
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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;">-ifneq ($(gaba),) # gaba source code directory</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CPPFLAGS += -DHAVE_GABA</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- INCLUDES += -I$(gaba)</span></span>
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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;">- LIBS_MORE += -L$(gaba)/build -lgaba</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CFLAGS += -msse4</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifneq ($(parasail),) # parasail install prefix</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;">- CPPFLAGS += -DHAVE_PARASAIL</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;">- INCLUDES += -I$(parasail)/include</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;">- LIBS_MORE += $(parasail)/lib/libparasail.a # don't link against the dynamic library</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifeq ($(sse2),)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CFLAGS += -march=native</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" 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="138" 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">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifneq ($(avx2),)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" 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">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CFLAGS += -mavx2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" 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="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.SUFFIXES:.c .o</span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" 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="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.c.o:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all:$(PROG)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" 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="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2-test:cli.o kalloc.o $(OBJS)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) $^ -o $@ $(LIBS_MORE) $(LIBS)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" 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="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="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="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM session*</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="155" 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">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-depend:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# DO NOT DELETE</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-cli.o: ksw2.h kseq.h</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-kalloc.o: kalloc.h</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_extd.o: ksw2.h</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_extd2_sse.o: ksw2.h</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_extf2_sse.o: ksw2.h</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_extz.o: ksw2.h</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_extz2_sse.o: ksw2.h</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_gg.o: ksw2.h</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_gg2.o: ksw2.h</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_gg2_sse.o: ksw2.h</span></span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#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">Makefile</span>.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">autoconf</span>.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#38a607d3983d0c698515dc04da7498f38de6df4d"><strong>debian/postinst</strong>
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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="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="k" style="font-weight: 600;">case</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">in</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>configure<span class="p">)</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"> <span class="p">;;</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> abort-upgrade|abort-remove|abort-deconfigure<span class="p">)</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="p">;;</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span><span class="p">)</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;">echo</span> <span class="s2" style="color: #d14;">"postinst called with unknown argument </span><span class="se" style="color: #d14;">\`</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">'"</span> <span class="o" style="font-weight: 600;">></span>&2</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;">exit </span>1</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"> <span class="p">;;</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">esac</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="c" style="color: #998; font-style: italic;">#DEBHELPER#</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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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exit </span>0</span></pre>
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<li id="4466ea135ee9e99902dde6a042ccca599e084c1d">
<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#4466ea135ee9e99902dde6a042ccca599e084c1d"><strong>debian/postrm</strong>
deleted
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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="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="k" style="font-weight: 600;">case</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">in</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>purge|remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear<span class="p">)</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"> <span class="p">;;</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"></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="p">)</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"postrm called with unknown argument </span><span class="se" style="color: #d14;">\`</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">'"</span> <span class="o" style="font-weight: 600;">></span>&2</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;">exit </span>1</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="p">;;</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">esac</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#DEBHELPER#</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exit </span>0</span></pre>
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<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#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">@@ -7,6 +7,11 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all</td>
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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"> dh $@</span>
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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">override_dh_auto_clean:</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> rm -f lib*so*</span></pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"># FIXME: I'd love to get rid of this dirty hack - but I have no better idea how to check for zlib</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">override_dh_autoreconf:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> ln -s /usr/share/aclocal/ax_check_zlib.m4 .</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> dh_autoreconf</span>
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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">override_dh_auto_install:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> dh_auto_install</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> rm ax_check_zlib.m4</span></pre>
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<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#a66dc2ea3b71d53e879ee60efe57194450fd06cb"><strong>debian/salsa-ci.yml.ex</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># For more information on what jobs are run see:</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># https://salsa.debian.org/salsa-ci-team/pipeline</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># To enable the jobs, go to your repository (at salsa.debian.org)</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># and click over Settings > CI/CD > Expand (in General pipelines).</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># In "Custom CI config path" write debian/salsa-ci.yml and click</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># in "Save Changes". The CI tests will run after the next commit.</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="elixir"><span class="o" style="font-weight: 600;">---</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="elixir"><span class="ss" style="color: #990073;">include:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="elixir"> <span class="o" style="font-weight: 600;">-</span> <span class="ss" style="color: #990073;">https:</span><span class="o" style="font-weight: 600;">//</span><span class="n" style="color: #333;">salsa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">salsa</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ci</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">team</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">raw</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">master</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">salsa</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ci</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">yml</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="elixir"> <span class="o" style="font-weight: 600;">-</span> <span class="ss" style="color: #990073;">https:</span><span class="o" style="font-weight: 600;">//</span><span class="n" style="color: #333;">salsa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">salsa</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ci</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">team</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">raw</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">master</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">jobs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#b8e122337dd307496078a30b70e46e5cf5c64f4b"><strong>debian/shlibs.local.ex</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="elixir"><span class="n" style="color: #333;">libksw2</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">20200514</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gitf06f9b3</span> <span class="n" style="color: #333;">ksw2</span> <span class="p">(</span><span class="o" style="font-weight: 600;">>></span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">20200514</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gitf06f9b3</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;">ksw2</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><<</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">20200514</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">gitf06f9b3</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">99</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> - Author: Suzuki, H. and Kasahara, M.</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Year: 2018</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Title: Introducing difference recurrence relations for faster semi-global alignment of long sequences.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> - Author: H. Suzuki and M. Kasahara</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: Introducing difference recurrence relations for faster semi-global alignment of long sequences</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Journal: BMC Bioinformatics</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Year: 2018</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Volume: 19</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> Pages: 45</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> DOI: 10.1186/s12859-018-2014-8 </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> PMID: 29504909</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> PMCID: PMC5836832</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> URL: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2014-8</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> eprint: https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2014-8</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> - Author: Li, H.</span>
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9
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> Year: 2018</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> Title: Minimap2: pairwise alignment for nucleotide sequences.</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> Journal: Bioinformatics</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> Volume: 34</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> Pages: 3094-3100</span></pre>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>
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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">opts="mode=git,pretty=0.0+git%cd.%h" \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/lh3/ksw2.git HEAD</span></pre>
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<a href="https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4#5d1f13dff4d26c5c7b8078725799f70441eb6bef"><strong>debian/watch.ex</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># Example watch control file for uscan</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># Rename this file to "watch" and then you can run the "uscan" command</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># to check for upstream updates and more.</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># See uscan(1) for format</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="elixir"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># Compulsory line, this is a version 4 file</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="elixir"><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="elixir"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># PGP signature mangle, so foo.tar.gz has foo.tar.gz.sig</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;">#opts="pgpsigurlmangle=s%$%.sig%"</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="elixir"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># HTTP site (basic)</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;">#http://example.com/downloads.html \</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># files/ksw2-([\d\.]+)\.tar\.gz debian uupdate</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="elixir"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># Uncomment to examine an FTP server</span></span>
</pre>
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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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<pre style="margin: 0;">-<span id="LC17" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;">#ftp://ftp.example.com/pub/ksw2-(.*)\.tar\.gz debian uupdate</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC18" class="line" lang="elixir"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC19" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># SourceForge hosted projects</span></span>
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<td class="diff-line-num old old_line" data-linenumber="20" 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">
20
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC20" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># http://sf.net/ksw2/ ksw2-(.*)\.tar\.gz debian uupdate</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="21" 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">
21
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC21" class="line" lang="elixir"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
22
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC22" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># GitHub hosted projects</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="23" 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">
23
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC23" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;">#opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%<project>-$1.tar.gz%" \</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="24" 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">
24
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC24" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># https://github.com/<user>/ksw2/tags \</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
25
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC25" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
26
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="elixir"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="27" 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">
27
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC27" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># PyPI</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="28" 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">
28
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC28" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># https://pypi.debian.net/ksw2/ksw2-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))</span></span>
</pre>
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<td class="diff-line-num old old_line" 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">
29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="elixir"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
30
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC30" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># Direct Git</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="31" 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">
31
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC31" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># opts="mode=git" http://git.example.com/ksw2.git \</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="32" 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">
32
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC32" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># refs/tags/v([\d\.]+) debian uupdate</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="33" 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">
33
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC33" class="line" lang="elixir"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
34
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC34" class="line" lang="elixir"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="35" 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">
35
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC35" class="line" lang="elixir"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="36" 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">
36
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC36" class="line" lang="elixir"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
37
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># Uncomment to find new files on GooglePages</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="38" 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">
38
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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC38" class="line" lang="elixir"><span class="c1" style="color: #998; font-style: italic;"># http://example.googlepages.com/foo.html ksw2-(.*)\.tar\.gz</span></span></pre>
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