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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/vmatch">Debian Med / vmatch</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vmatch/commit/4335f0f5adc7f3c672113a40e3bff18b207fd41a">4335f0f5</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-03T10:19:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix spelling in manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vmatch/commit/b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6">b309cc3b</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-03T10:26:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add patch headers
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c9840feea7bd248a5e5945c1d6bd1101fadd1800">
debian/mansrc/vmatch.1.adoc
</a>
</li>
<li class="file-stats">
<a href="#03a4d84e386afa1cd30b3b8f6060c14e4dd8ec44">
debian/mansrc/vmatchselect.1.adoc
</a>
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<li class="file-stats">
<a href="#c57ab768c760f529146250c68b4c58bbb66d1fe5">
debian/patches/common-distdir.patch
</a>
</li>
<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
debian/patches/hardening.patch
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</li>
<li class="file-stats">
<a href="#cd69b5be163c56a58505348802c679d4fd038191">
debian/patches/no-symlink.patch
</a>
</li>
<li class="file-stats">
<a href="#5f6a01555d0d62cc4825f3a9387c41598ada294c">
debian/patches/remove-hardcoded-includepaths.patch
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</li>
<li class="file-stats">
<a href="#89275d181d7aea320bd80cbebcb985b53857cb92">
debian/patches/skip-doc-installation.patch
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</li>
<li class="file-stats">
<a href="#ec69fc249c8cec85c5b8381611af04e6e8369991">
debian/patches/use-shared-gt-lib.patch
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</li>
</ul>
<h4>Changes:</h4>
<li id="c9840feea7bd248a5e5945c1d6bd1101fadd1800">
<a href="https://salsa.debian.org/med-team/vmatch/compare/5fc91a2e3775f1571a8a6e6bf8573dabc98cd666...b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6#c9840feea7bd248a5e5945c1d6bd1101fadd1800"><strong>debian/mansrc/vmatch.1.adoc</strong></a>
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<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,8 +23,8 @@ a combination of options specifying</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">* the output mode and output format.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Additionally, if there is more than one algorithm to solve a certain matching</span>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">task, *vmatch* allows <span class="idiff left right">to specify which algorithm is to be used. </span></span>
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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">
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">*vmatch* <span class="idiff left right">allows to compute</span> the following kinds of matches:</span>
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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">task, *vmatch* allows <span class="idiff left right">one to specify which algorithm is to be used.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">*vmatch* <span class="idiff left right">supports computing</span> the following kinds of matches:</span>
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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">. match all substrings of the database sequences against itself. The matches</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> can be one of the following kinds:</span>
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<li id="03a4d84e386afa1cd30b3b8f6060c14e4dd8ec44">
<a href="https://salsa.debian.org/med-team/vmatch/compare/5fc91a2e3775f1571a8a6e6bf8573dabc98cd666...b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6#03a4d84e386afa1cd30b3b8f6060c14e4dd8ec44"><strong>debian/mansrc/vmatchselect.1.adoc</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" 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">@@ -36,7 +36,7 @@ options specifying the index and/or the query sequences to be matched, as well</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">as options specifying how to match are not available in *vmatchselect*.</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">The options of *vmatchselect* have the same meaning as in the program *vmatch*.</span>
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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Thus, for a description, see the corresponding documentation. Note that</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">*vmatchselect* also <span class="idiff left right">allows to use</span> the option "-dbcluster". If *vmatchselect*</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">*vmatchselect* also <span class="idiff left right">supports</span> the option "-dbcluster". If *vmatchselect*</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">is called with this option, then it parses the given match file and performs</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">single linkage clustering based on the matches in this file.</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Thus *vmatch* and *vmatchselect* allow to perform hierarchical clustering.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" 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>
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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">@@ -44,7 +44,7 @@ In a first step an initial set of matches with loose matching criteria is</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">computed, using *vmatch*. Then one clusters these matches by calling</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">*vmatchselect*. In a second round one applies more strict choices for the</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">matches by the using the options "-l", "-leastscore", "-evalue", or</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">"-identity", etc. This <span class="idiff left right">allow</span>s stepwise refinement of clusters without much</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">"-identity", etc. This <span class="idiff left right">facilitate</span>s stepwise refinement of clusters without much</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">computational effort and no new index construction for the sequence of a</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">cluster. The output of *vmatchselect* is the same as the output of *vmatch*.</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"></span>
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<li id="c57ab768c760f529146250c68b4c58bbb66d1fe5">
<a href="https://salsa.debian.org/med-team/vmatch/compare/5fc91a2e3775f1571a8a6e6bf8573dabc98cd666...b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6#c57ab768c760f529146250c68b4c58bbb66d1fe5"><strong>debian/patches/common-distdir.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use a common dist directory</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-01-03</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -6,9 +6,8 @@</span></span>
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<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<a href="https://salsa.debian.org/med-team/vmatch/compare/5fc91a2e3775f1571a8a6e6bf8573dabc98cd666...b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Ensure that hardening flags get passed to the compiler calls</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-01-03</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/bin/mkfilegoals.pl</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/bin/mkfilegoals.pl</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -225,7 +225,7 @@</span></span>
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<a href="https://salsa.debian.org/med-team/vmatch/compare/5fc91a2e3775f1571a8a6e6bf8573dabc98cd666...b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6#cd69b5be163c56a58505348802c679d4fd038191"><strong>debian/patches/no-symlink.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Do not create symlinks</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-01-03</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/bin/mklink.sh</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/bin/mklink.sh</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>
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<li id="5f6a01555d0d62cc4825f3a9387c41598ada294c">
<a href="https://salsa.debian.org/med-team/vmatch/compare/5fc91a2e3775f1571a8a6e6bf8573dabc98cd666...b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6#5f6a01555d0d62cc4825f3a9387c41598ada294c"><strong>debian/patches/remove-hardcoded-includepaths.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: remove hardcoded include paths</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-01-03</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makedef-linux-gcc</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makedef-linux-gcc</span></span>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -15,9 +15,7 @@</span></span>
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<li id="89275d181d7aea320bd80cbebcb985b53857cb92">
<a href="https://salsa.debian.org/med-team/vmatch/compare/5fc91a2e3775f1571a8a6e6bf8573dabc98cd666...b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6#89275d181d7aea320bd80cbebcb985b53857cb92"><strong>debian/patches/skip-doc-installation.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Skip documentation installation (for now).</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-01-03</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">@@ -18<span class="idiff left right">7,9 +187</span>,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -18<span class="idiff left right">6,9 +186</span>,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> @cp Mkvtree/TRANS/Trans* $(VMATCHDISTDIR)/${SMAPDIR}</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> @cp bin/cleanpp.sh $(VMATCHDISTDIR)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> @cp bin/Vmatchtrans.pl $(VMATCHDISTDIR)</span>
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<li id="ec69fc249c8cec85c5b8381611af04e6e8369991">
<a href="https://salsa.debian.org/med-team/vmatch/compare/5fc91a2e3775f1571a8a6e6bf8573dabc98cd666...b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6#ec69fc249c8cec85c5b8381611af04e6e8369991"><strong>debian/patches/use-shared-gt-lib.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use Debian's libgenometools instead of static lib</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Vmatch was intended to be built as a static binary in a defined build</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> directory with a copy of libgenometools.a in a specific place.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> In Debian, we have a shared library, so let's use this in the build setup.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-01-03</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;">--- a/src/Mkvtree/Makefile</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;">+++ b/src/Mkvtree/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">@@ -1,10 +1,10 @@</span></span>
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