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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/jellyfish">Debian Med / jellyfish</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/commit/7ced039be20d272807a591f33caba3f89e38b844">7ced039b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-03T09:45:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Catch exceptions by reference
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/commit/12fb37bcae7426bfb1f51a892beb1cfd94ad5983">12fb37bc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-03T09:47:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enabling python bindings does not work - leave it as todo item
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/commit/69f40959442997142e115c4634999724d71f3963">69f40959</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-03T09:56:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not replace random '-L' strings in command line
</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#53f169f51304436a8e9879a3e78b8d5a09237bc7">
debian/README.todo
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#0dcc0785e9faa4c9073febbfac8afb1d62867ae0">
<span class="new-file">
+
debian/patches/fix_catch.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#243423a661123e892bf88eccb4eca29ccadb19cf">
<span class="new-file">
+
debian/patches/fix_replacement_of_-L_option.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="53f169f51304436a8e9879a3e78b8d5a09237bc7">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/ea26fa3aa9903765de174c706b905c3c2ac9cc1a...69f40959442997142e115c4634999724d71f3963#53f169f51304436a8e9879a3e78b8d5a09237bc7"><strong>debian/README.todo</strong></a>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,3 +3,5 @@ docs/ directory is out of date but regenerating it produces errors</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">ruby bindings break policy using upstream's install</span>
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<td class="diff-line-num new_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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">turning on the hardening options breaks the build</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="6" 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="7" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">python bindings for swig</span></pre>
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<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/ea26fa3aa9903765de174c706b905c3c2ac9cc1a...69f40959442997142e115c4634999724d71f3963#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" 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">@@ -5,8 +5,9 @@ jellyfish (2.2.10-1) UNRELEASED; urgency=medium</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.1.4</span>
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<td class="diff-line-num old_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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Adapt watch file to also catch v$VERSION tarball names</span>
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<td class="diff-line-num 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">
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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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Clean up quilt patches</span>
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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * Try to enable swig Python bindings</span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> TODO: ... but failed</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Catch exceptions by reference</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Do not replace random '-L' strings in command line</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Closes: #907819</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 03 Sep 2018 08:34:22 +0200</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<li id="0dcc0785e9faa4c9073febbfac8afb1d62867ae0">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/ea26fa3aa9903765de174c706b905c3c2ac9cc1a...69f40959442997142e115c4634999724d71f3963#0dcc0785e9faa4c9073febbfac8afb1d62867ae0"><strong>debian/patches/fix_catch.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Mon, 03 Sep 2018 08:34:22 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Catch exceptions by reference</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> see https://blog.knatten.org/2010/04/02/always-catch-exceptions-by-referenc</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></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;">--- a/sub_commands/count_main.cc</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sub_commands/count_main.cc</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -360,7 +360,7 @@ int count_main(int argc, char *argv[])</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> uint64_t max = args.upper_count_given ? args.upper_count_arg : std::numeric_limits<uint64_t>::max();</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> try {</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> merge_files(files, args.output_arg, header, min, max);</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } catch(MergeError e) {</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch(MergeError &e) {</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> err::die(err::msg() << e.what());</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"> if(!args.no_unlink_flag) {</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/include/jellyfish/hash_counter.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/include/jellyfish/hash_counter.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -213,7 +213,7 @@ protected:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> new_ary_ = new array(ary_->size(), ary_->key_len(), ary_->val_len() + 1,</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> ary_->max_reprobe(), ary_->reprobes());</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } catch(typename array::ErrorAllocation e) {</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch(typename array::ErrorAllocation &e) {</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> new_ary_ = 0;</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>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sub_commands/merge_main.cc</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sub_commands/merge_main.cc</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -33,7 +33,7 @@ int merge_main(int argc, char *argv[])</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> try {</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> merge_files(args.input_arg, args.output_arg, out_header, min, max);</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } catch(MergeError e) {</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch(MergeError &e) {</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> err::die(err::msg() << e.what());</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sub_commands/query_main.cc</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;">+++ b/sub_commands/query_main.cc</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -60,7 +60,7 @@ void query_from_cmdline(std::vector<cons</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> if(canonical)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> m.canonicalize();</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> out << m << " " << db.check(m) << "\n";</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } catch(std::length_error e) {</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch(std::length_error &e) {</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> std::cerr << "Invalid mer '" << *it << "'\n";</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -77,7 +77,7 @@ void query_from_stdin(const Database& db</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> if(canonical)</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> m.canonicalize();</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> out << db.check(m) << std::endl; // a flush is need for interactive use</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } catch(std::length_error e) {</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch(std::length_error &e) {</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> std::cerr << "Invalid mer '" << buffer << "'" << std::endl;</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> }</span></pre>
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<br>
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<li id="243423a661123e892bf88eccb4eca29ccadb19cf">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/ea26fa3aa9903765de174c706b905c3c2ac9cc1a...69f40959442997142e115c4634999724d71f3963#243423a661123e892bf88eccb4eca29ccadb19cf"><strong>debian/patches/fix_replacement_of_-L_option.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Do not replace random '-L' strings in command line</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/907819</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Last-Update: Mon, 03 Sep 2018 08:34:22 +0200</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></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;">--- a/examples/count_in_file/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/examples/count_in_file/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> CC = g++</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> CXXFLAGS = $(shell pkg-config --cflags jellyfish-2.0) -std=c++0x -Wall -O3</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LDFLAGS = -Wl,--rpath=$(shell pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L//g')</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;">+LDFLAGS = -Wl,--rpath=$(shell pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/ -L/ /g')</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> LDLIBS = $(shell pkg-config --libs jellyfish-2.0)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> all: count_in_file</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/examples/jf_count_dump/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/examples/jf_count_dump/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> CC = g++</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> CXXFLAGS = $(shell pkg-config --cflags jellyfish-2.0) -std=c++0x -Wall -O3</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LDFLAGS = -Wl,--rpath=$(shell pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L//g')</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS = -Wl,--rpath=$(shell pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/ -L/ /g')</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> LDLIBS = $(shell pkg-config --libs jellyfish-2.0)</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"> all: jf_count_dump</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;">--- a/examples/query_per_sequence/Makefile</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;">+++ b/examples/query_per_sequence/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> CC = g++</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> CXXFLAGS = $(shell pkg-config --cflags jellyfish-2.0) -std=c++0x -Wall -O3</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LDFLAGS = -Wl,--rpath=$(shell pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L//g')</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;">+LDFLAGS = -Wl,--rpath=$(shell pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/ -L/ /g')</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> LDLIBS = $(shell pkg-config --libs jellyfish-2.0)</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"> all: query_per_sequence</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;">--- a/swig/Tuprules.tup</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;">+++ b/swig/Tuprules.tup</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -80,7 +80,7 @@ endif</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> ifdef JELLYFISH_RPATH</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> JELLYFISH_RPATH = @(JELLYFISH_RPATH)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- JELLYFISH_RPATH = `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L/-Wl,-rpath,/g'`</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ JELLYFISH_RPATH = `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/ -L/ -Wl,-rpath,/g'`</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> ifdef RUBY_CFLAGS</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;">--- a/swig/perl5/Makefile.PL</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;">+++ b/swig/perl5/Makefile.PL</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -19,7 +19,7 @@ my $pkg = "jellyfish-2.0";</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> my $jf_cflags = pkgconfig("--cflags $pkg");</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> my $jf_libs = pkgconfig("--libs $pkg");</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> my $jf_rpath = pkgconfig("--libs-only-L $pkg");</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$jf_rpath =~ s/-L/-Wl,-rpath,/g;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$jf_rpath =~ s/ -L/ -Wl,-rpath,/g;</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> print("$jf_cflags\n$jf_libs\n$jf_rpath\n");</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/swig/ruby/extconf.rb</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/swig/ruby/extconf.rb</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -13,7 +13,7 @@ end</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> $defs << pkgconfig("--cflags jellyfish-2.0") << '-std=c++0x'</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> libs = [pkgconfig("--libs jellyfish-2.0"),</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pkgconfig("--libs-only-L jellyfish-2.0").gsub(/-L/, "-Wl,-rpath,")]</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pkgconfig("--libs-only-L jellyfish-2.0").gsub(/ -L/, " -Wl,-rpath,")]</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> if Array === $libs</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> $libs += libs</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/swig/python/setup.py</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/swig/python/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17,7 +17,7 @@ def pkgconfig(s):</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> jf_libs = [re.sub(r'-l', '', x) for x in pkgconfig("--libs-only-l jellyfish-2.0")]</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> jf_include = [re.sub(r'-I', '', x) for x in pkgconfig("--cflags-only-I jellyfish-2.0")]</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> jf_cflags = pkgconfig("--cflags-only-other jellyfish-2.0")</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-jf_libdir = [re.sub(r'-L', '', x) for x in pkgconfig("--libs-only-L jellyfish-2.0")]</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+jf_libdir = [re.sub(r' -L', ' ', x) for x in pkgconfig("--libs-only-L jellyfish-2.0")]</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> jf_rpath = [re.sub(r'^', '-Wl,-rpath,', x) for x in jf_libdir]</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> jf_ldflags = pkgconfig("--libs-only-other jellyfish-2.0")</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/jellyfish/compare/ea26fa3aa9903765de174c706b905c3c2ac9cc1a...69f40959442997142e115c4634999724d71f3963#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">manpage_whatis_entry.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">reproducible.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">portability.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">fix_catch.patch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">fix_replacement_of_-L_option.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/jellyfish/compare/ea26fa3aa9903765de174c706b905c3c2ac9cc1a...69f40959442997142e115c4634999724d71f3963#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -29,7 +29,7 @@ override_dh_install:</td>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> dh_auto_configure --sourcedirectory=swig/perl5</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> dh_auto_configure --sourcedirectory=swig/python</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"><span class="idiff left right">#</span> dh_auto_configure --sourcedirectory=swig/python</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> dh_auto_build --sourcedirectory=swig/perl5</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> dh_auto_install --sourcedirectory=swig/perl5</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" 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>
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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">@@ -42,7 +42,7 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> debian/tmp/usr/lib/*/lib$(DEB_SOURCE)-*.so</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> dh_auto_configure -- --enable-swig --enable-perl-binding --enable-python-binding</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> dh_auto_configure -- --enable-swig --enable-perl-binding <span class="idiff left right"># </span>--enable-python-binding</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">override_dh_clean:</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> dh_clean</span>
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