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<h3>
Michael R. Crusoe 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/6d79d5333ad03ed3bb6be9a598b5124ad365cea2">6d79d533</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-06T16:31:20Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.6</pre>
</li>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#2e62d67be9b972fb94be4079924f65c3df9a24ac">
gff_utils.cpp
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<li class="file-stats">
<a href="#037bd3173d312d85c9ae5e3fa8f48a79706aa6fb">
gffread.cpp
</a>
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<h4>Changes:</h4>
<li id="2e62d67be9b972fb94be4079924f65c3df9a24ac">
<a href="https://salsa.debian.org/med-team/gffread/commit/6d79d5333ad03ed3bb6be9a598b5124ad365cea2#2e62d67be9b972fb94be4079924f65c3df9a24ac"><strong>gff_utils.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="734" 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">@@ -734,7 +734,7 @@ void GffLoader::load(GList<GenomicSeqData>& seqdata, GFValidateFunc* gf_validate</td>
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734
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="cpp"> <span class="n" style="color: #333;">GffNameList</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">attrnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">attrs</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//gffr->names->attrs;</span></span>
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735
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735
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">attrnames</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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736
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736
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">attrnames</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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737
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">endsiWith</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left right">_</span>type"</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="738" 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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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">endsiWith</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="s" style="color: #d14;">"type"</span><span class="p">))</span> <span class="p">{</span></span>
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738
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="cpp"> <span class="n" style="color: #333;">pseudoTypeAttrIds</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">attrnames</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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739
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739
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="cpp"> <span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">// else {</span></span>
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740
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740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">strifind</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="s" style="color: #d14;">"pseudo"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="783" 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="783" 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">@@ -783,7 +783,7 @@ void GffLoader::load(GList<GenomicSeqData>& seqdata, GFValidateFunc* gf_validate</td>
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783
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783
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="n" style="color: #333;">warnPseudo</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="784" 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">
784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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785
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="cpp"> <span class="p">}</span></span>
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786
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<pre style="margin: 0;">-<span id="LC786" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// *<span class="idiff left right">_</span>type=*_pseudogene</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// *type=*_pseudogene</span></span>
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787
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//find all attributes ending with _type and have value like: *_pseudogene</span></span>
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788
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">pseudoTypeAttrIds</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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789
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">attrv</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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<a href="https://salsa.debian.org/med-team/gffread/commit/6d79d5333ad03ed3bb6be9a598b5124ad365cea2#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">5</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">6</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -100,7 +100,9 @@ Output options:\n\</td>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -g full path to a multi-fasta file with the genomic sequences\n\</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> for all input mappings, OR a directory with single-fasta files\n\</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> (one per genomic sequence, with file names matching sequence names)\n\</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -w write a fasta file with spliced exons for each GFF transcript\n\</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -w write a fasta file with spliced exons for each transcript\n\</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --w-add <N> for the -w option, extract additional <N> bases\n\</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> both upstream and downstream of the transcript boundaries\n\</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -x write a fasta file with spliced CDS for each GFF transcript\n\</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -y write a protein fasta file with the translation of CDS for each record\n\</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -W for -w and -x options, write in the FASTA defline the exon\n\</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="113" 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">@@ -111,8 +113,6 @@ Output options:\n\</td>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -m <chr_replace> is a name mapping table for converting reference \n\</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> sequence names, having this 2-column format:\n\</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> <original_ref_ID> <new_ref_ID>\n\</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> WARNING: all GFF records on reference sequences whose original IDs\n\</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> are not found in the 1st column of this table will be discarded!\n\</span></span>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -t use <trackname> in the 2nd column of each GFF/GTF output line\n\</span></span>
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117
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -o write the records into <outfile> instead of stdout\n\</span></span>
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118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -T main output will be GTF instead of GFF3\n\</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="184" 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">@@ -184,9 +184,10 @@ class CTableField {</td>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ffasta</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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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f_in</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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186
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</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="p">;</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">FILE</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="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//fasta with spliced exons (transcripts)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="188" 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">
188
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<td class="diff-line-num new_line old" data-linenumber="187" 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="LC188" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">FILE</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="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//fasta with spliced CDS</span></span>
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<td class="diff-line-num old old_line" data-linenumber="189" 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">
189
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<td class="diff-line-num new_line old" data-linenumber="187" 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="LC189" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">FILE</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 class="c1" style="color: #998; font-style: italic;">//fasta with translated CDS</span></span>
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<td class="diff-line-num new old_line" data-linenumber="190" 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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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">FILE</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="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//writing fasta with spliced exons (transcripts)</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">wPadding</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;">//padding for -w option</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">FILE</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="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//writing fasta with spliced CDS</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">FILE</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 class="c1" style="color: #998; font-style: italic;">//wrting fasta with translated CDS</span></span>
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190
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"></span>
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191
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">wCDSonly</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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192
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">wNConly</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="697" 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="698" 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">@@ -697,7 +698,21 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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697
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698
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">cds_start</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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698
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699
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">cds_end</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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699
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="cpp"> <span class="n" style="color: #333;">seglst</span><span class="p">.</span><span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//TODO: ? if wPadding is set, *temporarily* change first and last exon coordinates ?!?</span></span>
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// or perhaps getSpliced() should take an additional padding parameter ?!?</span></span>
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">padLeft</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">padRight</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wPadding</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="cpp"> <span class="n" style="color: #333;">padLeft</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">uint</span><span class="p">)</span><span class="n" style="color: #333;">wPadding</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">wPadding</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ediff</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">faseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getseqlen</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="cpp"> <span class="n" style="color: #333;">padRight</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">wPadding</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">ediff</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">ediff</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">wPadding</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="cpp"> <span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">addPadding</span><span class="p">(</span><span class="n" style="color: #333;">padLeft</span><span class="p">,</span> <span class="n" style="color: #333;">padRight</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">exont</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getSpliced</span><span class="p">(</span><span class="n" style="color: #333;">faseq</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cds_start</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cds_end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seglst</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//restore exons to normal (remove padding)</span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wPadding</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">removePadding</span><span class="p">(</span><span class="n" style="color: #333;">padLeft</span><span class="p">,</span> <span class="n" style="color: #333;">padRight</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">defline</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exont</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">CDstart</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="719" 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="734" 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">@@ -719,6 +734,13 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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719
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">);</span></span>
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720
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735
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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721
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736
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="cpp"> <span class="p">}</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wPadding</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="738" 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">
738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" padding:"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="739" 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">
739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">padLeft</span><span class="p">);</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span><span class="sc" style="color: #d14;">'|'</span><span class="p">;</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">padRight</span><span class="p">);</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"> <span class="p">}</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"></span>
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722
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744
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" segs:"</span><span class="p">);</span></span>
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723
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745
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">seglst</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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724
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746
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="727" 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="749" 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">@@ -727,6 +749,7 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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727
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749
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">seglst</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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728
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750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="cpp"> <span class="p">}</span></span>
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729
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp"> <span class="p">}</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="cpp"></span>
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730
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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731
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754
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//append all attributes found for each transcripts</span></span>
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732
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="844" 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">@@ -821,12 +844,13 @@ bool validateGffRec(GffObj* gffrec, GList<GffObj>* gfnew) {</td>
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821
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rt</span><span class="p">)</span> <span class="p">{</span></span>
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822
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="cpp"> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setRefName</span><span class="p">(</span><span class="n" style="color: #333;">rt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">new_name</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="823" 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">
823
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846
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="847" 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">
847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* //no, do not discard non-matching entries, let them pass through!</span></span>
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824
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<td class="diff-line-num new_line" data-linenumber="848" 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">
848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> else {</span></span>
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825
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<td class="diff-line-num new_line" data-linenumber="849" 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">
849
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (verbose)</span></span>
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826
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> GMessage("Info: %s discarded due to reference %s not being mapped\n",</span></span>
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<td class="diff-line-num old_line" data-linenumber="827" 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">
827
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851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> gffrec->getID(), refname.chars());</span></span>
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828
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852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return false; //discard, ref seq not in the given translation table</span></span>
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829
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="cpp"> <span class="p">}</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }<span class="idiff left right">*/</span></span></span>
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830
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854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="cpp"> <span class="p">}</span></span>
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831
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">transcriptsOnly</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isDiscarded</span><span class="p">())</span> <span class="p">{</span></span>
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832
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//discard generic "locus" features with no other detailed subfeatures</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1006" 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="1030" 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">@@ -1006,7 +1030,7 @@ void printAsTable(FILE* f, GffObj* gfo, int* out_counter=NULL) {</td>
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1006
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1030
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>
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1007
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1031
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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="cpp"> <span class="n" style="color: #333;">GArgs</span> <span class="n" style="color: #333;">args</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span></span>
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1008
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1032
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<pre style="margin: 0;"> <span id="LC1032" class="line" lang="cpp"> <span class="s" style="color: #d14;">"version;debug;merge;adj-stop;bed;in-bed;tlf;in-tlf;cluster-only;nc;cov-info;help;"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1009" 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">
1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sort-alpha;keep-genes;keep-comments;keep-exon-attrs;force-exons;t-adopt;gene2exon;"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1010" 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="1033" 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">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sort-alpha;keep-genes;<span class="idiff left right">w-add=;</span>keep-comments;keep-exon-attrs;force-exons;t-adopt;gene2exon;"</span></span>
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<td class="diff-line-num old_line" data-linenumber="1010" 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">
1010
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<td class="diff-line-num new_line" data-linenumber="1034" 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">
1034
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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ignore-locus;no-pseudo;table=sort-by=hvOUNHPWCVJMKQYTDARSZFGLEBm:g:i:r:s:l:t:o:w:x:y:d:"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1011" 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">
1011
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1035
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<pre style="margin: 0;"> <span id="LC1035" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="n" style="color: #333;">USAGE</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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1012
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<td class="diff-line-num new_line" data-linenumber="1036" 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">
1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'h'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1207" 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="1231" 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">@@ -1207,13 +1231,18 @@ int main(int argc, char* argv[]) {</td>
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1207
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<td class="diff-line-num new_line" data-linenumber="1231" 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">
1231
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<pre style="margin: 0;"> <span id="LC1231" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (f_out==NULL) f_out=stdout;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1208" 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">
1208
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<td class="diff-line-num new_line" data-linenumber="1232" 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">
1232
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<pre style="margin: 0;"> <span id="LC1232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gfasta</span><span class="p">.</span><span class="n" style="color: #333;">fastaPath</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="p">(</span><span class="n" style="color: #333;">validCDSonly</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">spliceCheck</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'w'</span><span class="p">)</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'x'</span><span class="p">)</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'y'</span><span class="p">)</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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<td class="diff-line-num old_line" data-linenumber="1209" 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">
1209
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<td class="diff-line-num new_line" data-linenumber="1233" 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">
1233
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<pre style="margin: 0;"> <span id="LC1233" class="line" lang="cpp"> <span class="n" style="color: #333;">GError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: -g option is required for options -w, -x, -y, -V, -N, -M !</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1210
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<td class="diff-line-num new_line old" data-linenumber="1234" 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="LC1210" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1211" 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">
1211
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<td class="diff-line-num new_line" data-linenumber="1234" 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">
1234
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<pre style="margin: 0;"> <span id="LC1234" class="line" lang="cpp"> <span class="n" style="color: #333;">openfw</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="sc" style="color: #d14;">'w'</span><span class="p">);</span></span>
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<td class="diff-line-num 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">
1212
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<td class="diff-line-num new_line" data-linenumber="1235" 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">
1235
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<pre style="margin: 0;"> <span id="LC1235" 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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<td class="diff-line-num new_line" data-linenumber="1236" 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">
1236
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<pre style="margin: 0;"> <span id="LC1236" 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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<td class="diff-line-num new old_line" data-linenumber="1214" 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="1237" 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">
1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"w-add"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1214" 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="1238" 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">
1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1214" 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="1239" 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">
1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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="p">)</span> <span class="n" style="color: #333;">GError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --w-add option requires -w option!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1240" 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">
1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="cpp"> <span class="n" style="color: #333;">wPadding</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">asInt</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1241" 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">
1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="cpp"> <span class="p">}</span></span>
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1214
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1242
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1215" 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">
1215
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<td class="diff-line-num new_line" data-linenumber="1243" 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">
1243
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<pre style="margin: 0;"> <span id="LC1243" 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="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">covInfo</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1216" 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">
1216
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<td class="diff-line-num new_line" data-linenumber="1244" 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">
1244
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<pre style="margin: 0;"> <span id="LC1244" 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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<td class="diff-line-num new old_line" data-linenumber="1217" 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="1245" 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">
1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="cpp"></span>
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1217
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<td class="diff-line-num new_line" data-linenumber="1246" 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">
1246
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<pre style="margin: 0;"> <span id="LC1246" 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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<td class="diff-line-num old_line" data-linenumber="1218" 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">
1218
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<pre style="margin: 0;"> <span id="LC1247" 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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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="cpp"></span>
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