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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/libmaus2">Debian Med / libmaus2</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/libmaus2/-/commit/be6f8364c812e75c44c9134e2cddf2d92690344f">be6f8364</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2020-11-18T15:30:41+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add spelling-error-in-header.patch
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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debian/patches/series
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debian/patches/spelling-error-in-header.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/be6f8364c812e75c44c9134e2cddf2d92690344f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libmaus2 (2.0.766+dfsg-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Add spelling-error-in-header.patch to fix spelling-error-in-binary affecting</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> biobambam2.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org> Wed, 18 Nov 2020 13:52:56 +0100</span>
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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">libmaus2 (2.0.766+dfsg-1) unstable; urgency=medium</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"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/be6f8364c812e75c44c9134e2cddf2d92690344f#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">spelling-error-in-header.patch</span></pre>
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<li id="3149275ef0f13c1af3e1564ce6f7db3ca07c2ab8">
<a href="https://salsa.debian.org/med-team/libmaus2/-/commit/be6f8364c812e75c44c9134e2cddf2d92690344f#3149275ef0f13c1af3e1564ce6f7db3ca07c2ab8"><strong>debian/patches/spelling-error-in-header.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix spelling error in header files</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> This is causing lintian reports spelling-error-in-binary in biobambam2.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2020-11-18</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</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;">--- libmaus2.orig/src/libmaus2/bambam/BamHeaderLowMem.hpp</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;">+++ libmaus2/src/libmaus2/bambam/BamHeaderLowMem.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -699,7 +699,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> if ( ! isi )</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> {</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> ::libmaus2::exception::LibMausException se;</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- se.getStream() << "BamHeaderLowMem: defect @PG line with non-existant parent " << std::string(text+parstart,text+parend) << ":\n" << PLA->getLine(text,lineid) << std::endl;</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;">+ se.getStream() << "BamHeaderLowMem: defect @PG line with non-existent parent " << std::string(text+parstart,text+parend) << ":\n" << PLA->getLine(text,lineid) << std::endl;</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> se.finish();</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> throw se;</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> }</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libmaus2.orig/src/libmaus2/bambam/HeaderLine.hpp</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;">+++ libmaus2/src/libmaus2/bambam/HeaderLine.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -129,7 +129,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> if ( ! hasKey(key) )</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> {</span>
</pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> ::libmaus2::exception::LibMausException se;</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- se.getStream() << "bambam::HeaderLine::getValue called for non existant key: " << key << " for line of type " << type << std::endl;</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;">+ se.getStream() << "bambam::HeaderLine::getValue called for non existent key: " << key << " for line of type " << type << std::endl;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> se.finish();</span>
</pre>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> throw se;</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> }</span>
</pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libmaus2.orig/src/libmaus2/fastx/FastABgzfIndex.hpp</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libmaus2/src/libmaus2/fastx/FastABgzfIndex.hpp</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -98,7 +98,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> if ( i < 0 )</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> {</span>
</pre>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> libmaus2::exception::LibMausException ex;</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ex.getStream() << "::libmaus2::fastx::FastABgzfIndexEntry::operator[] called for non existant id" << std::endl;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ex.getStream() << "::libmaus2::fastx::FastABgzfIndexEntry::operator[] called for non existent id" << std::endl;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> ex.finish();</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> throw ex;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libmaus2.orig/src/test/testAIO.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libmaus2/src/test/testAIO.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -255,7 +255,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> void testPosixFdOverwrite()</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std::string const fn = "nonexistant.test.file";</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::string const fn = "nonexistent.test.file";</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> std::string const text1 = "Hello world.";</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> std::string const text2 = "new text";</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span></pre>
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