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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/commit/02fa992d130157d967f8b87935f55e182bb5ab86">02fa992d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-12T16:29:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing Build-Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/commit/25b4d52baa6c68af0dac5a2ebe024acffd61740e">25b4d52b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-12T16:35:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install executables and docs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/commit/dadc58c195ab32c5f0ccd86bcadd4021d81629c9">dadc58c1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-12T16:40:49+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Propagare hardening options
</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="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
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+
debian/docs
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<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
<span class="new-file">
+
debian/install
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<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
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+
debian/patches/hardening.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/kma/compare/ece208df846de25f7c73580bd08f33f22f22d6e8...dadc58c195ab32c5f0ccd86bcadd4021d81629c9#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,7 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num new_line" data-linenumber="5" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<td class="diff-line-num new_line old" data-linenumber="6" 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="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~)</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> zlib1g-dev</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Standards-Version: 4.1.4</span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/kma</span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/kam.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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="17" 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">@@ -16,9 +17,8 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Description: mapping genomic sequences to raw reads directly against redundant databases</span>
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> KMA is mapping a method designed to map raw reads directly against</span>
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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"> redundant databases, in an ultra-fast manner using seed and extend. KMA</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> is particulary good at aligning high quality reads against highly</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> is particular<span class="idiff left right">l</span>y good at aligning high quality reads against highly</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> redundant databases, where unique matches often does not exist. It works</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> for long low quality reads as well, such as those from Nanopore. Non-</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> unique matches are resolved using the "ConClave" sorting scheme, and a</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> consensus sequence are outputtet in addition to other common attributes,</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> based on our users demands.</span></pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> consensus sequence are outputtet in addition to other common attributes.</span></pre>
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<a href="https://salsa.debian.org/med-team/kma/compare/ece208df846de25f7c73580bd08f33f22f22d6e8...dadc58c195ab32c5f0ccd86bcadd4021d81629c9#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">README*</span></pre>
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<a href="https://salsa.debian.org/med-team/kma/compare/ece208df846de25f7c73580bd08f33f22f22d6e8...dadc58c195ab32c5f0ccd86bcadd4021d81629c9#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kma usr/bin</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">kma_index usr/bin</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">kma_shm usr/bin</span></pre>
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<a href="https://salsa.debian.org/med-team/kma/compare/ece208df846de25f7c73580bd08f33f22f22d6e8...dadc58c195ab32c5f0ccd86bcadd4021d81629c9#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.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: Thu, 07 Jun 2018 21:55:00 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Propagate hardening options</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/Makefile</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/Makefile</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;">@@ -1,16 +1,16 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS = -std=c99 -w -O3</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 += -std=c99 -w -O3</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> BINS = kma kma_index kma_shm</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> all: $(BINS)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> kma: KMA.c</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) -o $@ $< -lm -lpthread -lz</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CFLAGS) -g -o $@ $< -lm -lpthread -lz $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> kma_index: KMA_index.c</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;">- $(CC) $(CFLAGS) -o $@ $< -lm</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;">+ $(CC) $(CFLAGS) -g -o $@ $< -lm $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> kma_shm: KMA_SHM.c</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) -o $@ $<</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CFLAGS) -g -o $@ $< $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> $(RM) $(BINS)</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/kma/compare/ece208df846de25f7c73580bd08f33f22f22d6e8...dadc58c195ab32c5f0ccd86bcadd4021d81629c9#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">hardening.patch</span></pre>
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