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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/libstatgen">Debian Med / libstatgen</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libstatgen/-/commit/641c2a4e1b2b3bec85adcb5971e15917cc4d4fcb">641c2a4e</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2021-08-21T10:40:06+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove merged patches
</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#8a9d631f678b5fbde28d1282cc2bd62957406388">
<span class="deleted-file">
−
debian/patches/Fix_compilation_error.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#44109d6bc03ee640bcf8b8f14a80e25f9d314a0e">
debian/patches/Fix_compilation_flags.patch
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</li>
<li class="file-stats">
<a href="#623279b3a4d0885b8a1e749df98126efb5474148">
<span class="deleted-file">
−
debian/patches/Remove_erroneous_deletes_in_Chromosome_constructor.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libstatgen/-/commit/641c2a4e1b2b3bec85adcb5971e15917cc4d4fcb#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,6 +6,7 @@ libstatgen (1.0.15-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> [ Dylan Aïssi ]</span>
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<td class="new_line diff-line-num" 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" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Remove merged patches</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"> -- Dylan Aïssi <daissi@debian.org> Sat, 21 Aug 2021 10:34:47 +0200</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<li id="8a9d631f678b5fbde28d1282cc2bd62957406388">
<a href="https://salsa.debian.org/med-team/libstatgen/-/commit/641c2a4e1b2b3bec85adcb5971e15917cc4d4fcb#8a9d631f678b5fbde28d1282cc2bd62957406388"><strong>debian/patches/Fix_compilation_error.patch</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Fix some compilation errors.</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Bug: https://github.com/statgen/libStatGen/issues/15</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> https://github.com/statgen/libStatGen/issues/17</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Origin: https://github.com/statgen/libStatGen/commit/2f1876e</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> https://github.com/statgen/libStatGen/commit/9db9c23</span>
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<td class="old_line diff-line-num 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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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> https://github.com/statgen/libStatGen/commit/5500464</span>
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<td class="old_line diff-line-num old" data-linenumber="7" 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="LC7" class="line" lang="diff"> https://github.com/statgen/libStatGen/commit/198a43e</span>
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<td class="old_line diff-line-num old" data-linenumber="8" 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="new_line diff-line-num old" data-linenumber="0" 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="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">--- a/general/Parameters.cpp</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/general/Parameters.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -553,7 +553,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> int line_len = 0;</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"> bool legacy_parameters = false;</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;">- bool legacy_count = 0;</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;">+ int legacy_count = 0;</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"> for (LongParameterList * ptr = list + 1; ptr->description != NULL; ptr++)</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> if (ptr->type == LP_LEGACY_PARAMETERS)</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/general/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/general/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="p">@@ -8,7 +8,10 @@</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> # an error, but allow unused results and variables for the</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> # time being.</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"><span class="gd" style="color: #000; background-color: #fdd;">- USER_WARNINGS ?= -Werror $(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-strict-overflow" ; fi)</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Disable format-truncation check because StringBasics specifically tests</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # to make sure snprintf truncates as expected.</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ USER_WARNINGS ?= -Werror -Wno-format-truncation $(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-strict-overflow" ; fi) </span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# USER_WARNINGS ?= -Werror $(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-strict-overflow" ; fi)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> #-Wno-strict-overflow</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> # -Wno-unused-variable $(shell if [ X$(CCVERSION) \> X4.2.0 ] ; then echo " -Wno-unused-result" ; fi)</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> endif</span></pre>
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<li id="44109d6bc03ee640bcf8b8f14a80e25f9d314a0e">
<a href="https://salsa.debian.org/med-team/libstatgen/-/commit/641c2a4e1b2b3bec85adcb5971e15917cc4d4fcb#44109d6bc03ee640bcf8b8f14a80e25f9d314a0e"><strong>debian/patches/Fix_compilation_flags.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" 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="11" 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">@@ -11,7 +11,7 @@ Description: Add -fPIC to build the shared library.</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> OPTFLAG_DEBUG?=-ggdb -O0</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> OPTFLAG_PROFILE?=-pg</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">59</span>,9 +<span class="idiff right">59</span>,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">67</span>,9 +<span class="idiff right">67</span>,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> REQ_SETTINGS = </span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </span>
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<li id="623279b3a4d0885b8a1e749df98126efb5474148">
<a href="https://salsa.debian.org/med-team/libstatgen/-/commit/641c2a4e1b2b3bec85adcb5971e15917cc4d4fcb#623279b3a4d0885b8a1e749df98126efb5474148"><strong>debian/patches/Remove_erroneous_deletes_in_Chromosome_constructor.patch</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: jonathonl <jonathonl@users.noreply.github.com></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Date: Thu, 20 Sep 2018 11:57:06 -0400</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Origin: https://github.com/statgen/libStatGen/commit/3a10afe08c209dbacc3eca7794a5a8c0a42ee566</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Bug-Debian: https:bugs.debian.org/905368</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Subject: Removes erroneous deletes in Chromosome constructor.</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">---</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> general/Chromosome.cpp | 2 --</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> 1 file changed, 2 deletions(-)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff">diff --git a/general/Chromosome.cpp b/general/Chromosome.cpp</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">index ac2ff5c..2d773e8 100644</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/general/Chromosome.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/general/Chromosome.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="p">@@ -27,7 +27,6 @@</span> Chromosome::Chromosome(GenomeSequence* gs, const char* chromosomeName)</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace) </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"> std::string s(genomseSequenceFileName);</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;">- if (this->gs) delete gs;</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> gs = new GenomeSequence;</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> assert(gs);</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> gs->setReferenceName(s);</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="p">@@ -39,7 +38,6 @@</span> Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromos</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> Chromosome::Chromosome(const std::string& genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace) </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (this->gs) delete gs;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> gs = new GenomeSequence;</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> assert(gs);</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> gs->setReferenceName(genomseSequenceFileName);</span></pre>
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<a href="https://salsa.debian.org/med-team/libstatgen/-/commit/641c2a4e1b2b3bec85adcb5971e15917cc4d4fcb#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Fix_compilation_error.patch</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Fix_compilation_flags.patch</span></pre>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Remove_erroneous_deletes_in_Chromosome_constructor.patch</span></pre>
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