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<h3>
Steffen Möller pushed to branch upstream
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/2148d2d567ed992121ed34af206dfb6425e50f5b">2148d2d5</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-01-27T11:04:01+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.7</pre>
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<h4>1 changed file:</h4>
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<a href="#037bd3173d312d85c9ae5e3fa8f48a79706aa6fb">
gffread.cpp
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<h4>Changes:</h4>
<li id="037bd3173d312d85c9ae5e3fa8f48a79706aa6fb">
<a href="https://salsa.debian.org/med-team/gffread/commit/2148d2d567ed992121ed34af206dfb6425e50f5b#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">6</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">7</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="126" 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="126" 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">@@ -126,7 +126,8 @@ Output options:\n\</td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --table output a simple tab delimited format instead of GFF, with columns\n\</span></span>
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<td class="diff-line-num old_line" data-linenumber="127" 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="LC127" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> having the values of GFF attributes given in <attrlist>; special\n\</span></span>
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<td class="diff-line-num old_line" data-linenumber="128" 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="LC128" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> pseudo-attributes (prefixed by @) are recognized:\n\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="129" 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="LC129" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen\n\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" 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="LC129" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, \n\</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> @cds, @covlen, @cdslen\n\</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -v,-E expose (warn about) duplicate transcript IDs and other potential\n\</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> problems with the given GFF/GTF records\n\</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" 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="160" 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">@@ -159,7 +160,8 @@ class RefTran {</td>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">ETableFieldType</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_Attr</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// attribute name as is</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//ID or @id</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//ID or @id or transcript_id</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//geneID or @gene_id</span></span>
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163
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<td class="diff-line-num new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//Parent or @parent</span></span>
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164
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<td class="diff-line-num new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_chr</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@chr</span></span>
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165
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_feature</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@feature</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="293" 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="295" 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">@@ -293,6 +295,7 @@ void setTableFormat(GStr& s) {</td>
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293
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ETableFieldType</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">specialFields</span><span class="p">;</span></span>
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294
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"chr"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_chr</span><span class="p">));</span></span>
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295
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"id"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="298" 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">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"geneid"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">));</span></span>
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296
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"parent"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">));</span></span>
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297
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"feature"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_feature</span><span class="p">));</span></span>
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298
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_start</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="317" 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="320" 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">@@ -317,11 +320,16 @@ void setTableFormat(GStr& s) {</td>
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317
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">GMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: table field '@%s' not recognized!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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318
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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319
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="p">}</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"ID"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="323" 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">
323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"ID"</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">w</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="s" style="color: #d14;"><span class="idiff right">"transcript_id"</span></span><span class="p">)</span> <span class="p">{</span></span>
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321
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">tcol</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">);</span></span>
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322
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tcol</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="323" 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">
323
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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324
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<td class="diff-line-num new_line" data-linenumber="327" 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">
327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="328" 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">
328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"geneID"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"gene_id"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="329" 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">
329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">tcol</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="330" 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">
330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tcol</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="331" 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">
331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="332" 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">
332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="325" 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">
325
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<td class="diff-line-num new_line" data-linenumber="333" 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">
333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"Parent"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="326" 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">
326
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<td class="diff-line-num new_line" data-linenumber="334" 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">
334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">tcol</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="327" 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">
327
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<td class="diff-line-num new_line" data-linenumber="335" 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">
335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tcol</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="951" 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="959" 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">@@ -951,6 +959,9 @@ void printGxfTab(FILE* f, GffObj& g) {</td>
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<td class="diff-line-num old_line" data-linenumber="951" 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">
951
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<td class="diff-line-num new_line" data-linenumber="959" 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">
959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="952" 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">
952
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<td class="diff-line-num new_line" data-linenumber="960" 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">
960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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<td class="diff-line-num old_line" data-linenumber="953" 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">
953
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<td class="diff-line-num new_line" data-linenumber="961" 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">
961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="954" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="962" 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">
962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="954" 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="963" 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">
963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getGeneID</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="954" 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="964" 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">
964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="954" 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">
954
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<td class="diff-line-num new_line" data-linenumber="965" 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">
965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="955" 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">
955
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<td class="diff-line-num new_line" data-linenumber="966" 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">
966
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC966" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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<td class="diff-line-num old_line" data-linenumber="956" 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">
956
</td>
<td class="diff-line-num new_line" data-linenumber="967" 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">
967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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