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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libedlib">Debian Med / libedlib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/commit/bac479c8ce4d81027d46ad4ac006e5286a1402b7">bac479c8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-09T21:52:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add edlib-aligner package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/commit/00b390bcbbc51ae32cb5f4cb8b3ba33aa3a279e2">00b390bc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-09T21:55:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not build helloWorld, DEP3
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#5a3cef95340d1d44275bd1903d087f906abc41b0">
<span class="new-file">
+
debian/edlib-aligner.install
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</li>
<li class="file-stats">
<a href="#8faf0ddd3cd26e1f5838988db13ac9df6caba67a">
<span class="new-file">
+
debian/patches/do_not_build_hello_example.patch
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</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#787efc042d800d77574619c4ebb6b86074732323">
debian/patches/soversion.patch
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</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libedlib/compare/266a42d360cd7557fde7d39cf28b95d540155082...00b390bcbbc51ae32cb5f4cb8b3ba33aa3a279e2#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,3 +73,29 @@ Description: library for sequence alignment using edit distance (devel)</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> * Super fast thanks to Myers's bit-vector algorithm.</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"> This package contains the static library and the header files.</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">Package: edlib-aligner</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> libedlib0 (= ${binary:Version})</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">Description: edlib sequence alignment tool using edit distance</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> Edlib is a lightweight and super fast C/C++ library for sequence</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> alignment using edit distance. This package provides an aligner</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> using this library.</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> Features of libedlib</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> * Calculates edit distance (Levehnstein distance).</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> * It can find optimal alignment path (instructions how to transform</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> first sequence into the second sequence).</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> * It can find just the start and/or end locations of alignment path -</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> can be useful when speed is more important than having exact</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> alignment path.</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> * Supports multiple alignment methods: global(NW), prefix(SHW) and</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> infix(HW), each of them useful for different scenarios.</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> * You can extend character equality definition, enabling you to e.g.</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> have wildcard characters, to have case insensitive alignment or to</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> work with degenerate nucleotides.</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> * It can easily handle small or very large sequences, even when finding</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> alignment path, while consuming very little memory.</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> * Super fast thanks to Myers's bit-vector algorithm.</span></pre>
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<li id="5a3cef95340d1d44275bd1903d087f906abc41b0">
<a href="https://salsa.debian.org/med-team/libedlib/compare/266a42d360cd7557fde7d39cf28b95d540155082...00b390bcbbc51ae32cb5f4cb8b3ba33aa3a279e2#5a3cef95340d1d44275bd1903d087f906abc41b0"><strong>debian/edlib-aligner.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">edlib</span><span class="o" style="font-weight: 600;">-</span><span class="nx">aligner</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/compare/266a42d360cd7557fde7d39cf28b95d540155082...00b390bcbbc51ae32cb5f4cb8b3ba33aa3a279e2#8faf0ddd3cd26e1f5838988db13ac9df6caba67a"><strong>debian/patches/do_not_build_hello_example.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Fri, 08 Jun 2018 13:20:51 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: helloWorld example does not properly build ... but why should we?</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -50,8 +50,8 @@ target_include_directories(edlib_static</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> $<INSTALL_INTERFACE:include>)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> # Build binaries.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_executable(helloWorld apps/hello-world/helloWorld.c)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-target_link_libraries(helloWorld edlib_static)</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;">+#add_executable(helloWorld apps/hello-world/helloWorld.c)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#target_link_libraries(helloWorld edlib_static)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> add_executable(runTests test/runTests.cpp)</span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="diff"> target_link_libraries(runTests edlib_static)</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/libedlib/compare/266a42d360cd7557fde7d39cf28b95d540155082...00b390bcbbc51ae32cb5f4cb8b3ba33aa3a279e2#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">soversion.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">do_not_build_hello_example.patch</span></pre>
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<li id="787efc042d800d77574619c4ebb6b86074732323">
<a href="https://salsa.debian.org/med-team/libedlib/compare/266a42d360cd7557fde7d39cf28b95d540155082...00b390bcbbc51ae32cb5f4cb8b3ba33aa3a279e2#787efc042d800d77574619c4ebb6b86074732323"><strong>debian/patches/soversion.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Fri, 08 Jun 2018 13:20:51 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Add soversion</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,5 +1,5 @@</span></span>
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