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GitLab

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<h3>

Sascha Steinbiss pushed to branch master

at <a href="https://salsa.debian.org/med-team/genometools">Debian Med / genometools</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/genometools/-/commit/bb3bf8ab616752843b8cf4915e9998e3827198f4">bb3bf8ab</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2020-07-22T13:33:29+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add patch to fix build on GCC10

</pre>

</li>

</ul>

<h4>4 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#2b74f32a7f92773f8a255f183fe932e83d2ee910">

debian/patches/adding_soname

</a>

</li>

<li class="file-stats">

<a href="#81a9a5b123fb5e9473f68e4733e9d389fa7872c9">

<span class="new-file">

+

debian/patches/gcc10.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/genometools/-/commit/bb3bf8ab616752843b8cf4915e9998e3827198f4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">genometools (1.6.1+ds-3) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Add patch to fix build on GCC 10.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">    Closes: #957268</span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Sascha Steinbiss <satta@debian.org>  Wed, 22 Jul 2020 13:00:06 +0200</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">genometools (1.6.1+ds-2) unstable; urgency=medium</span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * Use static images for AnnotationSketch documentation.</span>

</pre>

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<br>

</li>

<li id="2b74f32a7f92773f8a255f183fe932e83d2ee910">

<a href="https://salsa.debian.org/med-team/genometools/-/commit/bb3bf8ab616752843b8cf4915e9998e3827198f4#2b74f32a7f92773f8a255f183fe932e83d2ee910"><strong>debian/patches/adding_soname</strong></a>

<hr>

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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="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">@@ -25,7 +25,7 @@ Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de></td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" class="line" lang="diff"> define PROGRAM_template</span>

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<td class="diff-line-num old_line" data-linenumber="27" 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="LC27" class="line" lang="diff"> $(1): $(2)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">1003,7 +1005</span>,8 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">999,7 +1001</span>,8 @@</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff">  $(RANLIB) $(prefix)/lib/libgenometools.a</span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> endif</span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> ifneq ($(sharedlib),no)</span>

</pre>

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<br>

</li>

<li id="81a9a5b123fb5e9473f68e4733e9d389fa7872c9">

<a href="https://salsa.debian.org/med-team/genometools/-/commit/bb3bf8ab616752843b8cf4915e9998e3827198f4#81a9a5b123fb5e9473f68e4733e9d389fa7872c9"><strong>debian/patches/gcc10.patch</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From 51205942b1f41abdf841771deac4e0e35d7d5016 Mon Sep 17 00:00:00 2001</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Sascha Steinbiss <satta@debian.org></span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Wed, 22 Apr 2020 21:59:57 +0200</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH 1/2] make sure to not ignore snprintf output</span></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">GCC 10 will warn about the (here intended) silent string truncation</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">done by snprintf() unless the return value is handled.</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Obviously this will break the build as we use -Werror. We</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">circumvent the problem by checking the output value and printing a</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">warning if we notice a truncation.</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">---</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> src/ltr/ltrdigest_file_out_stream.c | 17 ++++++++++++-----</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> 1 file changed, 12 insertions(+), 5 deletions(-)</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">diff --git a/src/ltr/ltrdigest_file_out_stream.c b/src/ltr/ltrdigest_file_out_stream.c</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">index 723b8cf9a..61325b693 100644</span></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/src/ltr/ltrdigest_file_out_stream.c</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/src/ltr/ltrdigest_file_out_stream.c</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></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"><span class="gd" style="color: #000; background-color: #fdd;">-  Copyright (c) 2008-2015 Sascha Steinbiss <sascha@steinbiss.name></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" 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="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Copyright (c) 2008-2020 Sascha Steinbiss <sascha@steinbiss.name></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="diff">   Copyright (c) 2008-2013 Center for Bioinformatics, University of Hamburg</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff">   Permission to use, copy, modify, and distribute this software for any</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -33,6 +33,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> #include "core/symbol.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> #include "core/undef_api.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> #include "core/unused_api.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "core/warning_api.h"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> #include "extended/extract_feature_sequence.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> #include "extended/feature_node.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> #include "extended/feature_node_iterator_api.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -416,6 +417,8 @@</span> int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff">     if (!had_err) {</span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff">       GtRange rng;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      int ret = 0;</span></span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff">       ls->element.seqid = gt_calloc((size_t) ls->seqnamelen+1, sizeof (char));</span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff">       (void) snprintf(ls->element.seqid,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff">                       GT_MIN((size_t) gt_str_length(sdesc),</span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -425,12 +428,16 @@</span> int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)</span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff">       if (gt_str_length(sdesc) > (GtUword) ls->seqnamelen)</span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff">         ls->element.seqid[ls->seqnamelen] = '\0';</span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      (void) gt_ltrelement_format_description(&ls->element,</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                              ls->seqnamelen,</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                              desc,</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                              (size_t) (GT_MAXFASTAHEADER-1));</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      ret = gt_ltrelement_format_description(&ls->element,</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                             ls->seqnamelen,</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                             desc,</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;">+                                             (size_t) (GT_MAXFASTAHEADER-1));</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;">+      if (ret < 0) {</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        gt_warning("FASTA header truncated: %s", desc);</span></span>

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<pre style="margin: 0;">+<span id="LC57" 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="LC58" class="line" lang="diff">       gt_str_delete(sdesc);</span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC60" 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="LC61" class="line" lang="diff">       /* output basic retrotransposon data */</span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff">       lltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftLTR);</span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff">       rltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightLTR);</span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff">From 30ae36037228dc4ed174e8462f3489638e6f5e76 Mon Sep 17 00:00:00 2001</span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">From: Sascha Steinbiss <satta@debian.org></span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">Date: Wed, 22 Apr 2020 22:01:00 +0200</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">Subject: [PATCH 2/2] declare hashmap type as extern</span></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff">This fixes a build issue with GCC 10.</span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="p">Closes #941.</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">---</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> src/mgth/metagenomethreader.h | 2 +-</span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> 1 file changed, 1 insertion(+), 1 deletion(-)</span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff">diff --git a/src/mgth/metagenomethreader.h b/src/mgth/metagenomethreader.h</span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gh" style="color: #999;">index 92f16d498..7f76fffb9 100644</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/mgth/metagenomethreader.h</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/mgth/metagenomethreader.h</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="p">@@ -221,7 +221,7 @@</span> typedef struct</span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> } ParseStruct;</span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> </span>

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<td class="diff-line-num new new_line" data-linenumber="83" 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">

83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> /* specific access mode of queryhash */</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" 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">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp,,)</span></span>

</pre>

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85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp, extern,)</span></span>

</pre>

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86

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> DECLARE_SAFE_DEREF(GtUword *, ulp)</span>

</pre>

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87

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="88" 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">

88

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> /* Funktion, mit der der Metagenomethreader gestartet wird</span></pre>

</td>

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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/genometools/-/commit/bb3bf8ab616752843b8cf4915e9998e3827198f4#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,3 +7,4 @@ split-manuals</td>

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7

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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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">use-mx32</span>

</pre>

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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">

8

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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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">gtdoc-traverse-sorted</span>

</pre>

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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">

9

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<td class="diff-line-num new_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">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">ignore-m32-m64.patch</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" 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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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">gcc10.patch</span></pre>

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