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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/gffread">Debian Med / gffread</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/commit/c63dc927e39e88691fd768cbe96ec58aeac340db">c63dc927</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-25T07:16:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add breaks/replaces on cufflinks (<< 2.2.1+dfsg.1-4)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/commit/4bae3dc5e01aa6da25a05ac8ce9e0e16d63c5e5a">4bae3dc5</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-25T07:17:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.5</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/commit/e51443021dde77de1a220fd4e6b9978f059c9327">e5144302</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-25T07:17:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.11.5'
Update to upstream version '0.11.5'
with Debian dir 8253c6bf8ddaa2e7488e04350dbd548455ba6fed</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/commit/09fd781a907e6793307ef3e10af44948b8a3ba6e">09fd781a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-25T07:17:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/commit/86ea01c9b999f6e040d3f8bbbde841ad3c12a269">86ea01c9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-25T07:17:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Name.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/commit/0a7e42844e7825aaf7104a3284163f79c1754c9b">0a7e4284</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-25T07:19:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/commit/0f80bc9ffadf202e6aff51526fcc7f6075d58788">0f80bc9f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-25T07:28:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">refresh patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/commit/5293edc8ac00e41d2a8954d19ad5a49459de2e8f">5293edc8</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-25T07:36:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">improve hardening
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#3631b3210de1caa2caafc8366d6efc6d87696ea3">
debian/patches/gclib.patch
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<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
<span class="new-file">
+
debian/patches/hardening
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<li class="file-stats">
<a href="#037bd3173d312d85c9ae5e3fa8f48a79706aa6fb">
gffread.cpp
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/gffread/compare/6e69d38cf1bbe630b8b0824547f380691684e1e7...5293edc8ac00e41d2a8954d19ad5a49459de2e8f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gffread (0.11.5-1) UNRELEASED; urgency=medium</span>
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<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"> * New upstream release.</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"> * Add breaks/replaces on cufflinks (<< 2.2.1+dfsg.1-4). (Closes: #940915)</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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Set upstream metadata fields: Name.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Wed, 25 Sep 2019 09:15:58 +0200</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">gffread (0.11.4-2) unstable; urgency=medium</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"> [ Helmut Grohne ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/gffread/compare/6e69d38cf1bbe630b8b0824547f380691684e1e7...5293edc8ac00e41d2a8954d19ad5a49459de2e8f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,6 +14,8 @@ Package: gffread</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Breaks: cufflinks (<< 2.2.1+dfsg.1-4)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Replaces: cufflinks (<< 2.2.1+dfsg.1-4)</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Description: GFF/GTF format conversions, region filtering, FASTA sequence extraction</span>
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18
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> Gffread is a GFF/GTF parsing utility providing format conversions,</span>
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19
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> region filtering, FASTA sequence extraction and more.</span></pre>
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<li id="3631b3210de1caa2caafc8366d6efc6d87696ea3">
<a href="https://salsa.debian.org/med-team/gffread/compare/6e69d38cf1bbe630b8b0824547f380691684e1e7...5293edc8ac00e41d2a8954d19ad5a49459de2e8f#3631b3210de1caa2caafc8366d6efc6d87696ea3"><strong>debian/patches/gclib.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">@@ -2,9 +2,9 @@ Author: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Thu, 18 Apr 2019 12:40:25 +0200</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Fix build against libgclib</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">a</span>/Makefile</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>/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left">2,8 +82,8 @@</span></span><span class="idiff right"> gffread.o : gff_utils.h $(GCLDIR)/GBase.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">gffread.orig</span>/Makefile</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">gffread</span>/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left right">3,8 +83,8 @@</span></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> gff_utils.o : gff_utils.h $(GCLDIR)/gff.h</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> ${GCLDIR}/gff.o : ${GCLDIR}/gff.h ${GCLDIR}/GFaSeqGet.h ${GCLDIR}/GList.hh ${GCLDIR}/GHash.hh</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> ${GCLDIR}/GFaSeqGet.o : ${GCLDIR}/GFaSeqGet.h</span>
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<li id="d6c09299b1f914372840e8fd6fcc850f8a11b236">
<a href="https://salsa.debian.org/med-team/gffread/compare/6e69d38cf1bbe630b8b0824547f380691684e1e7...5293edc8ac00e41d2a8954d19ad5a49459de2e8f#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Use CPPFLAGS</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Allows Debian to harden the binary with CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2</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;">--- gffread.orig/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;">+++ gffread/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -65,7 +65,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> %.o : %.cpp</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;">- ${CXX} ${CXXFLAGS} -c $< -o $@</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;">+ ${CXX} ${CPPFLAGS} ${CXXFLAGS} -c $< -o $@</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> # C/C++ linker</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/gffread/compare/6e69d38cf1bbe630b8b0824547f380691684e1e7...5293edc8ac00e41d2a8954d19ad5a49459de2e8f#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">gclib.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">hardening</span></pre>
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<a href="https://salsa.debian.org/med-team/gffread/compare/6e69d38cf1bbe630b8b0824547f380691684e1e7...5293edc8ac00e41d2a8954d19ad5a49459de2e8f#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> - Name: OMICtools</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Entry: OMICS_28050</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Entry: gffread</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Name: OMICtools</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Entry: OMICS_28050</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Entry: gffread</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Name: gffread</span></pre>
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<a href="https://salsa.debian.org/med-team/gffread/compare/6e69d38cf1bbe630b8b0824547f380691684e1e7...5293edc8ac00e41d2a8954d19ad5a49459de2e8f#037bd3173d312d85c9ae5e3fa8f48a79706aa6fb"><strong>gffread.cpp</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">@@ -4,7 +4,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define __STDC_FORMAT_MACROS</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <inttypes.h></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "0.11.<span class="idiff left right">4</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "0.11.<span class="idiff left right">5</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define USAGE "gffread v" VERSION ". Usage:\n\</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] \n\</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1212" 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="1212" 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">@@ -1212,7 +1212,7 @@ int main(int argc, char* argv[]) {</td>
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1212
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1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="cpp"> <span class="n" style="color: #333;">openfw</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1213" 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">
1213
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1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="cpp"> <span class="n" style="color: #333;">openfw</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="sc" style="color: #d14;">'y'</span><span class="p">);</span></span>
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1214
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1214
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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="cpp"></span>
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1215
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<pre style="margin: 0;">-<span id="LC1215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_w</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_x</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_y</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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1215
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_w</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_x</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_y</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff right">covInfo</span></span><span class="p">)</span></span>
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1216
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1216
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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="cpp"> <span class="n" style="color: #333;">f_out</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stdout</span><span class="p">;</span></span>
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1217
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1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (f_y!=NULL || f_x!=NULL) wCDSonly=true;</span></span>
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1218
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1218
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//useBadCDS=useBadCDS || (fgtfok==NULL && fgtfbad==NULL && f_y==NULL && f_x==NULL);</span></span>
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