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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>
</h3>
<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/libmaus2/-/commit/131bd6981129d41efeb5ae5ac54e9d3a564d64a8">131bd698</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-06-28T20:03:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix-test-on-32bits.patch forwarded
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<strong><a href="https://salsa.debian.org/med-team/libmaus2/-/commit/5a1936a109d75ba11277ae497f26e04807c1caa7">5a1936a1</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-06-29T00:28:58+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">spelling-error-in-header.patch applied upstream
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<strong><a href="https://salsa.debian.org/med-team/libmaus2/-/commit/d25d20509eeaa4dac12f4eb198c437db65d32ad5">d25d2050</a></strong>
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<span>by Étienne Mollier</span>
<i>at 2021-06-29T00:31:49+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ready for upload to experimental
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#c9104c993096f4cd26431d43c7968739446feb1c">
debian/patches/fix-test-on-32bits.patch
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<a href="#3149275ef0f13c1af3e1564ce6f7db3ca07c2ab8">
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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/-/compare/f1346d5ddfe72f803a11d7d57448811f862266de...d25d20509eeaa4dac12f4eb198c437db65d32ad5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">libmaus2 (2.0.791+dfsg-1<span class="idiff left right">) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libmaus2 (2.0.791+dfsg-1<span class="idiff left right">~0exp0) experimental</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"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * d/control: updated my uploader address</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * add fix-test-on-32bits.patch; fix FTBFS on i386</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * removed spelling-error-in-header.patch; applied upstream</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> <span class="idiff left">Sun</span>, 2<span class="idiff">7</span> Jun 2021 0<span class="idiff right">9:55:25</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> <span class="idiff left">Tue</span>, 2<span class="idiff">9</span> Jun 2021 0<span class="idiff right">0:02:08</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">libmaus2 (2.0.768+dfsg-2) unstable; urgency=medium</span>
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<td class="new_line diff-line-num" data-linenumber="12" 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="LC12" class="line" lang="plaintext"></span>
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<li id="c9104c993096f4cd26431d43c7968739446feb1c">
<a href="https://salsa.debian.org/med-team/libmaus2/-/compare/f1346d5ddfe72f803a11d7d57448811f862266de...d25d20509eeaa4dac12f4eb198c437db65d32ad5#c9104c993096f4cd26431d43c7968739446feb1c"><strong>debian/patches/fix-test-on-32bits.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: fix test breaking due to type mismatch on 32 bits platforms</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">no</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">https://gitlab.com/german.tischler/libmaus2/-/issues/35</span></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-06-27</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC6" 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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<a href="https://salsa.debian.org/med-team/libmaus2/-/compare/f1346d5ddfe72f803a11d7d57448811f862266de...d25d20509eeaa4dac12f4eb198c437db65d32ad5#3149275ef0f13c1af3e1564ce6f7db3ca07c2ab8"><strong>debian/patches/spelling-error-in-header.patch</strong>
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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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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> ::libmaus2::exception::LibMausException se;</span>
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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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<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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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> se.finish();</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> throw se;</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> }</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;">--- 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>
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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>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> se.finish();</span>
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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>
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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>
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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>
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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>
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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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