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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/sniffles">Debian Med / sniffles</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sniffles/-/commit/40d369f7d1d59d2b5909e70793480e21ae8e40e5">40d369f7</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-11-27T23:36:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream accepted patch. New version.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sniffles/-/commit/8ac1729c698b65b81032f6574c8960db2412e03b">8ac1729c</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-11-27T23:37:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.12b+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sniffles/-/commit/62a65df58966f762cc740fc36d47f5ec0b98a3b6">62a65df5</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-11-27T23:37:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.0.12b+ds'
Update to upstream version '1.0.12b+ds'
with Debian dir b85b890c43d09df1f2bffb55c5503bdd8e883da0</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#56f8179db1634b6dd860eca5b9ee2ac0f92f2673">
<span class="new-file">
+
debian/patches/stoppingRecursion.patch
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<li class="file-stats">
<a href="#46a0eac0df27bbdf49c8effa7531b4766967e289">
src/Paramer.h
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/sniffles/-/compare/2e3595cf6e0bdc972fb214bb16612243ba1a36cc...62a65df58966f762cc740fc36d47f5ec0b98a3b6#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,9 +7,9 @@ option(STATIC "Build static binary" OFF)</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SNIF_VERSION_MINOR 0 <span class="p">)</span></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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span><span class="p">(</span>CMAKE_BUILD_TYPE STREQUAL <span class="s2" style="color: #d14;">"Debug"</span><span class="p">)</span></span>
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<td class="diff-line-num old_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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span>STATUS <span class="s2" style="color: #d14;">"Building in debug mode!"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SNIF_VERSION_BUILD 1<span class="idiff left right">1</span>-debug <span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="11" 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="LC10" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SNIF_VERSION_BUILD 1<span class="idiff left right">2</span>-debug <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SNIF_VERSION_BUILD 1<span class="idiff left right">1</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> SNIF_VERSION_BUILD 1<span class="idiff left right">2</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ENDIF</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"></span>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/2e3595cf6e0bdc972fb214bb16612243ba1a36cc...62a65df58966f762cc740fc36d47f5ec0b98a3b6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">sniffles (1.0.12<span class="idiff left right">+ds-1) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sniffles (1.0.12<span class="idiff left right">b+ds-1) unstable</span>; urgency=medium</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"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> * <span class="idiff left right">TODO/BLOCKER: Wait for reaction of upstream to https://github.com/fritzsedlazeck/Sniffles/pull/225</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * <span class="idiff left right">Fixed d/watch to also accept a-z updates</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Wed, 02 Sep 2020 20:48:13 +0200</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/2e3595cf6e0bdc972fb214bb16612243ba1a36cc...62a65df58966f762cc740fc36d47f5ec0b98a3b6#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">external-libs.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">no-extra-binary.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">stoppingRecursion.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/2e3595cf6e0bdc972fb214bb16612243ba1a36cc...62a65df58966f762cc740fc36d47f5ec0b98a3b6#56f8179db1634b6dd860eca5b9ee2ac0f92f2673"><strong>debian/patches/stoppingRecursion.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Fixing recursion - accepted upstream</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forward: https://github.com/fritzsedlazeck/Sniffles/pull/225</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sniffles/src/tree/Intervall_bed.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</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;">--- sniffles.orig/src/tree/Intervall_bed.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sniffles/src/tree/Intervall_bed.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -80,9 +80,9 @@</span> bool IntervallTree_bed::is_in(long posit</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> long score = p->overlap(position);</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> if (score > 0) {</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;">- is_in(position, p->left);</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;">+ return(is_in(position, p->left));</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> } else if (score < 0) {</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;">- is_in(position, p->right);</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;">+ return(is_in(position, p->right));</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> return true;</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/2e3595cf6e0bdc972fb214bb16612243ba1a36cc...62a65df58966f762cc740fc36d47f5ec0b98a3b6#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="repack,repacksuffix=+ds,dversionmangle=s/\+ds\d*$//,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%sniffles-$1.tar.gz%" \</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> https://github.com/fritzsedlazeck/sniffles/tags \</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> (?:.*?/)?v?(\d[\d.]*)\.tar\.gz</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="repack,repacksuffix=+ds,dversionmangle=auto,filenamemangle=s%(?:.*?)?v(\d[\d.]*[a-z]?)\.tar\.gz%sniffles-$1.tar.gz%" \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/fritzsedlazeck/Sniffles/tags (?:.*?/)?v(\d[\d.]*[a-z]?)\.tar\.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/2e3595cf6e0bdc972fb214bb16612243ba1a36cc...62a65df58966f762cc740fc36d47f5ec0b98a3b6#46a0eac0df27bbdf49c8effa7531b4766967e289"><strong>src/Paramer.h</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">@@ -25,7 +25,7 @@ class Parameter {</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="nl">private:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">Parameter</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">window_thresh</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//TODO check!</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1.0.1<span class="idiff left right">1</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1.0.1<span class="idiff left right">2</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">huge_ins</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">999</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//TODO check??</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">Parameter</span><span class="p">()</span> <span class="p">{</span></span>
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