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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libssw">Debian Med / libssw</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libssw/-/commit/61429a6e909c53aced3d9bcd60d2a74d528afe9f">61429a6e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-23T09:09:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop symbol from symbols file that is not created by gcc-10
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libssw/-/commit/4695c0ce3835b13b9cc9599b6995841ba32fb419">4695c0ce</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-23T10:44:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Restore build_all_libs.patch to build properly soversioned shared lib as well as static lib
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libssw/-/commit/c2c568647338036513f688cdd8171d551134a7ad">c2c56864</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-23T10:46:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#c5af7795298462d6fb2e3c1446ce9d7ee521d8a0">
debian/libssw0.symbols
</a>
</li>
<li class="file-stats">
<a href="#75de8a8fba7b2dc8f523b991ff6a523ed2bf920f">
debian/patches/build_all_libs.patch
</a>
</li>
<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
debian/patches/hardening.patch
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<li class="file-stats">
<a href="#52dc3e58185a550acb60dd82bc30b7c62d391abb">
debian/patches/rename_tool.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libssw/-/compare/a19c146931e078e0e56abc85684f5a3583165e63...c2c568647338036513f688cdd8171d551134a7ad#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="plaintext">libssw (1.1-10) <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">libssw (1.1-10) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="2" 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="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Team upload</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<td class="diff-line-num old_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">
3
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<td class="diff-line-num 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Improve crossbuilding</span>
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<td class="diff-line-num old_line" data-linenumber="4" 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="diff-line-num 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">
7
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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"> * Add "nojava" build profile</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">
8
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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"> * Add salsa-ci file (routine-update)</span>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +10,11 @@ libssw (1.1-10) UNRELEASED; urgency=medium</td>
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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"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<td class="diff-line-num old_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="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> Repository-Browse.</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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<td class="diff-line-num new_line" 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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<td class="diff-line-num new_line old" data-linenumber="13" 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="LC10" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 16 Feb 2020 17:23:59 +0100</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * Drop symbol from symbols file that is not created by gcc-10</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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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> Closes: #957481</span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 23 Jul 2020 10:44:14 +0200</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">libssw (1.1-9) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/libssw/-/compare/a19c146931e078e0e56abc85684f5a3583165e63...c2c568647338036513f688cdd8171d551134a7ad#c5af7795298462d6fb2e3c1446ce9d7ee521d8a0"><strong>debian/libssw0.symbols</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">@@ -22,7 +22,6 @@ libssw.so.0 libssw0 #MINVER#</td>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> _ZNK20StripedSmithWaterman7Aligner5AlignEPKcRKNS_6FilterEPNS_9AlignmentE@Base 1.1</span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> _ZNK20StripedSmithWaterman7Aligner5AlignEPKcS2_RKiRKNS_6FilterEPNS_9AlignmentE@Base 1.1</span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> _ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_@Base 1.1</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> _ZNSt6vectorIjSaIjEEaSERKS1_@Base 1.1</span>
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26
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev@Base 1.1</span>
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27
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev@Base 1.1</span>
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28
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev@Base 1.1</span>
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<li id="75de8a8fba7b2dc8f523b991ff6a523ed2bf920f">
<a href="https://salsa.debian.org/med-team/libssw/-/compare/a19c146931e078e0e56abc85684f5a3583165e63...c2c568647338036513f688cdd8171d551134a7ad#75de8a8fba7b2dc8f523b991ff6a523ed2bf920f"><strong>debian/patches/build_all_libs.patch</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">@@ -4,9 +4,17 @@ Description: build all libraries</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> Not upstreamed as upstream intends their C source to be inlined with the</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> code using the functions.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <sascha@steinbiss.name></span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libssw.orig/src/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libssw/src/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -10,8 +10,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -5,24 +5,29 @@</span> CXXFLAGS := $(CFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> LOBJS = ssw.o</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> LCPPOBJS = ssw_cpp.o</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> PROG = ssw_test</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LIB = libssw.so</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SOVERS=.0</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LIB = libssw.so$(SOVERS)</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;">+STATICLIB = libssw.a</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> EXAMPLE = example_c</span>
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10
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> EXAMPLE_CPP = example_cpp</span>
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11
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> JAVA_JAR = ssw.jar</span>
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12
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> JAVA_LIB = libsswjni.so</span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="25" 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">@@ -17,7 +25,10 @@ Author: Sascha Steinbiss <sascha@steinbiss.name></td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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18
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> .PHONY: all default java clean</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="p">@@ -21,8 +21,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-default: $(PROG) $(EXAMPLE) $(EXAMPLE_CPP) $(LIB) </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;">+default: $(PROG) $(EXAMPLE) $(EXAMPLE_CPP) $(LIB) $(STATICLIB)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> all: default java</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> java: $(JAVA_JAR) $(JAVA_LIB)</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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="36" 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">@@ -25,10 +36,13 @@ Author: Sascha Steinbiss <sascha@steinbiss.name></td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) -fPIC -shared -rdynamic -o $@ $<</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$(STATICLIB): $(LOBJS) $(LCPPOBJS)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ar rcs $@ $^</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> $(PROG): main.c kseq.h</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="LC31" class="line" lang="diff"><span class="p">@@ -38,10 +<span class="idiff left right">38,10 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -38,10 +<span class="idiff left">43,10 @@</span></span><span class="idiff right"> $(JAVA_LIB): sswjni.c ssw.c ssw.h</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> $(CC) $(CFLAGS) $(JAVA_INLCUDES) -fPIC -shared -rdynamic -o $@ $< ssw.c </span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> $(JAVA_JAR): $(JAVA_OBJ)</span>
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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">@@ -41,7 +55,7 @@ Author: Sascha Steinbiss <sascha@steinbiss.name></td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> ssw.o: ssw.c ssw.h</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> $(CC) -c -o $@ $< $(CFLAGS)</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="p">@@ -50,4 +5<span class="idiff left right">0,4 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -50,4 +5<span class="idiff left">5,4 @@</span></span><span class="idiff right"> ssw_cpp.o: ssw_cpp.cpp ssw_cpp.h ssw.h</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> $(CXX) -c -o $@ $< $(CXXFLAGS)</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> clean:</span>
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<li id="4d4a394ff4174f20019a8af4d8b6185efe92c21f">
<a href="https://salsa.debian.org/med-team/libssw/-/compare/a19c146931e078e0e56abc85684f5a3583165e63...c2c568647338036513f688cdd8171d551134a7ad#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: add hardening</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <sascha@steinbiss.name></span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">libssw.orig</span>/src/Makefile</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">libssw</span>/src/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/src/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">@@ -1,7 +1,8 @@</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;">-CC = gcc</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CXX = g++</span></span>
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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">@@ -15,20 +15,21 @@ Author: Sascha Steinbiss <sascha@steinbiss.name></td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> LOBJS = ssw.o</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> LCPPOBJS = ssw_cpp.o</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> PROG = ssw_test</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left right">2,20 +23,20 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left">4,7 +25,7 @@</span></span><span class="idiff right"> all: default java</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> java: $(JAVA_JAR) $(JAVA_LIB)</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> $(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^ $(LDFLAGS)</span></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"> $(PROG): main.c kseq.h</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="LC25" class="line" lang="diff"> $(STATICLIB): $(LOBJS) $(LCPPOBJS)</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> ar rcs $@ $^</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -34,13 +35,13 @@</span> $(PROG): main.c kseq.h</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> $(EXAMPLE): example.c</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"> $(PROG) $(EXAMPLE): $(LOBJS)</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) -o $@ $(filter-out %.h,$^) $(CFLAGS) -lm -lz</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;">+ $(CC) -o $@ $(filter-out %.h,$^) $(C<span class="idiff left right">PPFLAGS) $(C</span>FLAGS) -lm -lz $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) -o $@ $(filter-out %.h,$^) $(C<span class="idiff left right">FLAGS) $(CPP</span>FLAGS) -lm -lz $(LDFLAGS)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> $(EXAMPLE_CPP): example.cpp $(LOBJS) $(LCPPOBJS)</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) -o $@ $^ $(CXXFLAGS) -lm -lz</span></span>
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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">@@ -40,7 +41,7 @@ Author: Sascha Steinbiss <sascha@steinbiss.name></td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> $(JAVA_JAR): $(JAVA_OBJ)</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> jar cvf $@ $^</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left right">4,10 +45,10 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left">9,10 +50,10 @@</span></span><span class="idiff right"> $(JAVA_JAR): $(JAVA_OBJ)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> javac -target 1.6 -source 1.6 $<</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"> ssw.o: ssw.c ssw.h</span>
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<li id="52dc3e58185a550acb60dd82bc30b7c62d391abb">
<a href="https://salsa.debian.org/med-team/libssw/-/compare/a19c146931e078e0e56abc85684f5a3583165e63...c2c568647338036513f688cdd8171d551134a7ad#52dc3e58185a550acb60dd82bc30b7c62d391abb"><strong>debian/patches/rename_tool.patch</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">@@ -2,20 +2,20 @@ Description: build command line aligner</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> This patch ensures that 'ssw_test' is called 'ssw-align' in Debian</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> and also links against libssw.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Author: Sascha Steinbiss <satta@debian.org></span></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;">--- <span class="idiff left right">libssw.orig</span>/src/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;">+++ <span class="idiff left right">libssw</span>/src/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -5,7 +5,7 @@</span></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;">--- <span class="idiff left right">a</span>/src/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;">+++ <span class="idiff left right">b</span>/src/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -5,7 +5,7 @@</span><span class="idiff left right"> AR ?= ar</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> #CXXFLAGS := $(CFLAGS)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> LOBJS = ssw.o</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> LCPPOBJS = ssw_cpp.o</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PROG = ssw_test</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PROG = ssw-align</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> <span class="idiff left right">LIB = libssw.so</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> <span class="idiff left right">EXAMPLE = example_c</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> <span class="idiff left right">EXAMPLE_CPP = example_cpp</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">25,11 +25,12 @@</span></span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> $(<span class="idiff left right">LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> <span class="idiff left right">$(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^ $(LDFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> <span class="idiff left right">SOVERS=.0</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> <span class="idiff left right">LIB = libssw.so$(SOVERS)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> <span class="idiff left right">STATICLIB = libssw.a</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">30,11 +30,12 @@</span></span><span class="idiff right"> $(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cp</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> $(<span class="idiff left right">STATICLIB): $(LOBJS) $(LCPPOBJS)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> <span class="idiff left right">ar rcs $@ $^</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$(PROG): main.c kseq.h</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;">+$(PROG): main.c kseq.h $(LIB)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,12 +25,12 @@ Author: Sascha Steinbiss <satta@debian.org></td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$(PROG) $(EXAMPLE): $(LOBJS)</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$(EXAMPLE): $(LOBJS)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> $(CC) -o $@ $(filter-out %.h,$^) $(C<span class="idiff left right">PPFLAGS) $(C</span>FLAGS) -lm -lz $(LDFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> $(CC) -o $@ $(filter-out %.h,$^) $(C<span class="idiff left right">FLAGS) $(CPP</span>FLAGS) -lm -lz $(LDFLAGS)</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"> $(EXAMPLE_CPP): example.cpp $(LOBJS) $(LCPPOBJS)</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">libssw.orig</span>/src/main.c</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">libssw</span>/src/main.c</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="p">@@ -297,7 +297,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/src/main.c</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/main.c</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -297,7 +297,7 @@</span><span class="idiff left right"> int main (int argc, char * const argv[])</span></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"> if (optind + 2 > argc) {</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> fprintf(stderr, "\n");</span>
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