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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/gff2aplot">Debian Med / gff2aplot</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/gff2aplot/-/commit/ad844bca4bb553cd49c1af15e6629360f508f50d">ad844bca</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-06-14T11:55:03+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replace tabs in gff files with spaces
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#da5ee1a481077c6ac848a904ae89593faaee4e30">
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+
debian/patches/fix_gff_comments.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/gff2aplot/-/commit/ad844bca4bb553cd49c1af15e6629360f508f50d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gff2aplot (2.0-13) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Replace tabs in gff files with spaces (Closes: #962553)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Sun, 14 Jun 2020 11:51:26 +0530</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">gff2aplot (2.0-12) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Nelson A. de Oliveira retired from Debian (thanks for your previous</span>
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<li id="da5ee1a481077c6ac848a904ae89593faaee4e30">
<a href="https://salsa.debian.org/med-team/gff2aplot/-/commit/ad844bca4bb553cd49c1af15e6629360f508f50d#da5ee1a481077c6ac848a904ae89593faaee4e30"><strong>debian/patches/fix_gff_comments.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Replace tabs in gff files with spaces</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> GFFparsers are supposed to ignore all the text in lines that start with # but </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> for some reason, gffread doesn't like tabs in comments.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> The number of tabs after which gffread complains seems to be related to the </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> following line, but since this is just a comment anyway, replacing tabs with</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> spaces seems like an easier fix.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Author: Pranav Ballaney</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Bug-Debian: #962553</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Last-Update: 2020-06-14</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></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;">--- a/examples/mhcregion/hs-mm.gff</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;">+++ b/examples/mhcregion/hs-mm.gff</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> ##date Jun/03/2003 15:19:51</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> ##</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> ##/home/ug/jabril/development/softjabril/gfftools/gff2aplot/bin/ali2gff -x X87344 -y AF100956+AF027865 hs-mm.sim</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#name1:name2 source feature beg1:beg2 end1:end2 score strand frame group comment</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#name1:name2 source feature beg1:beg2 end1:end2 score strand frame group comment</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> X87344:AF100956+AF027865 sim96_LIN seqbounds 1:1 32000:35000 . . .</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> X87344:AF100956+AF027865 sim96_LIN alignment 863:804 19762:20115 18340.000 +:+ .:.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> X87344:AF100956+AF027865 sim96_LIN fragment 863:804 890:831 0.790 +:+ .:. ## cumulative nmp: 0.001</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;">--- a/examples/mhcregion/hs-mm.sim.gff</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;">+++ b/examples/mhcregion/hs-mm.sim.gff</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> ##date Jun/03/2003 16:41:22</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"> ## ali2gff -x X87344 -y AF100956+AF027865 hs-mm.sim</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#name1:name2 source feature beg1:beg2 end1:end2 score strand frame group comment</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#name1:name2 source feature beg1:beg2 end1:end2 score strand frame group comment</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> X87344:AF100956+AF027865 sim96_LIN seqbounds 1:1 32000:35000 . . .</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> X87344:AF100956+AF027865 sim96_LIN alignment 863:804 19762:20115 18340.000 +:+ .:.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> X87344:AF100956+AF027865 sim96_LIN fragment 863:804 890:831 0.790 +:+ .:. ## cumulative nmp: 0.001</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/gff2aplot/-/commit/ad844bca4bb553cd49c1af15e6629360f508f50d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -8,3 +8,4 @@ perl_5.28.patch</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">fix_install_ali2gff.patch</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">enhance_sprintf_buffer.patch</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">fix_README_used_for_test.patch</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">fix_gff_comments.patch</span></pre>
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