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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/gmap">Debian Med / gmap</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/f262b91c3454421731c6c3ccfee1a6754aef795b">f262b91c</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-11-24T21:54:57+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2020-11-20+ds</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#21fa3a3235386f70fbec47c2f55d39928abcbcca">
src/get-genome.c
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<a href="#d747f527041a6e797f86fcd6f1fcd1562bab24a2">
src/gmap.c
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<li class="file-stats">
<a href="#67480aa11532f910477b929399a61a7147daec47">
src/inbuffer.c
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<li class="file-stats">
<a href="#e1e0f0c720a674bf1a10020268eee09c7b9bc9ab">
src/inbuffer.h
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<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/gmap/-/commit/f262b91c3454421731c6c3ccfee1a6754aef795b#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="">2020-11-20 twu</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang=""> * index.html: Updated for latest version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang=""> * VERSION: Updated version number</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang=""> * get-genome.c: Added option --transcriptdb to get-genome to retrieve a gene</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang=""> structure</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang=""> * gmap.c: Using new interface to Inbuffer_setup</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang=""> * inbuffer.c, inbuffer.h: Providing NULL as arguments for genome and</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang=""> genomealt to Request_new</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="">2020-11-15 twu</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang=""> * substring.c: Checking that pos5 < pos3 before Substring trim procedures</span>
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<a href="https://salsa.debian.org/med-team/gmap/-/commit/f262b91c3454421731c6c3ccfee1a6754aef795b#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2020-11-14</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2020-11-20</span></pre>
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<a href="https://salsa.debian.org/med-team/gmap/-/commit/f262b91c3454421731c6c3ccfee1a6754aef795b#21fa3a3235386f70fbec47c2f55d39928abcbcca"><strong>src/get-genome.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: get-genome.c 223<span class="idiff left right">511 2020-11-14 15:50:08</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: get-genome.c 223<span class="idiff left right">600 2020-11-21 04:21:32</span>Z twu $"</span><span class="p">;</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -53,6 +53,8 @@ static bool coordp = false;</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"><span class="k" style="font-weight: 600;">static</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;">genomesubdir</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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54
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="k" style="font-weight: 600;">static</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;">dbroot</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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55
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="k" style="font-weight: 600;">static</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;">dbversion</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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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"><span class="k" style="font-weight: 600;">static</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;">transcriptome_dbroot</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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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"></span>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"><span class="k" style="font-weight: 600;">static</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;">user_typestring</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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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">wraplength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">60</span><span class="p">;</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"><span class="k" style="font-weight: 600;">static</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;">header</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -90,6 +92,7 @@ static struct option long_options[] = {</td>
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90
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Input options */</span></span>
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91
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"dir"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'D'</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* user_genomedir */</span></span>
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92
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"db"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'d'</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* dbroot */</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"transcriptdb"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* transcriptome_dbroot */</span></span>
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93
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"genes"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* genes_file_p */</span></span>
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94
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Output options */</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">@@ -160,10 +163,12 @@ Input options\n\</td>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"><span class="s" style="color: #d14;"> -D, --dir=STRING Genome directory</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"><span class="s" style="color: #d14;"> -d, --db=STRING Genome database. If argument is '?' (with</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"><span class="s" style="color: #d14;"> the quotes), this command lists available databases.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c"><span class="s" style="color: #d14;"> -c, --transcriptdb=STRING</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c"><span class="s" style="color: #d14;"> Retrieve the gene structure of the given contig argument</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"><span class="s" style="color: #d14;"> (Assumes transcriptome was built with gmap_build -c)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"><span class="s" style="color: #d14;"> --genes Argument is a genes file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"><span class="s" style="color: #d14;">Output options</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c"><span class="s" style="color: #d14;"> -2, --dibase Use dibase version of genome</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"><span class="s" style="color: #d14;"> -C, --coords Show coordinates only</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"><span class="s" style="color: #d14;"> -U, --uppercase Convert sequence to uppercase</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"><span class="s" style="color: #d14;"> -l, --wraplength=INT Wrap length for sequence (default=60)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</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">@@ -953,7 +958,7 @@ main (int argc, char *argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">long_option_index</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="LC959" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</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;">long_name</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC956" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</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 class="s" style="color: #d14;">"D:d:CUl:h:V:v:f:M:m:kru:ESALI^?"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</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 class="s" style="color: #d14;">"D:d:<span class="idiff left right">c:</span>CUl:h:V:v:f:M:m:kru:ESALI^?"</span><span class="p">,</span></span>
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957
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="c"> <span class="n" style="color: #333;">long_options</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">long_option_index</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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958
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963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">)</span> <span class="p">{</span></span>
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959
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<td class="diff-line-num new_line" data-linenumber="964" 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">
964
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<pre style="margin: 0;"> <span id="LC964" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1016" 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">@@ -1011,6 +1016,7 @@ main (int argc, char *argv[]) {</td>
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1011
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<td class="diff-line-num new_line" data-linenumber="1016" 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">
1016
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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="c"> <span class="n" style="color: #333;">dbroot</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="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">CALLOC</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="1012" 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">
1012
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<td class="diff-line-num new_line" data-linenumber="1017" 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">
1017
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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">dbroot</span><span class="p">,</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1013" 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">
1013
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<td class="diff-line-num new_line" data-linenumber="1018" 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">
1018
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<pre style="margin: 0;"> <span id="LC1018" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1014" 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="1019" 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">
1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">:</span> <span class="n" style="color: #333;">transcriptome_dbroot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1014
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<td class="diff-line-num new_line" data-linenumber="1020" 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">
1020
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<pre style="margin: 0;"> <span id="LC1020" class="line" lang="c"></span>
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<td class="diff-line-num old_line" data-linenumber="1015" 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">
1015
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<td class="diff-line-num new_line" data-linenumber="1021" 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">
1021
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'C'</span><span class="p">:</span> <span class="n" style="color: #333;">coordp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1016" 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">
1016
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<td class="diff-line-num new_line" data-linenumber="1022" 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">
1022
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'U'</span><span class="p">:</span> <span class="n" style="color: #333;">uppercasep</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1051" 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="1057" 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">@@ -1051,6 +1057,33 @@ main (int argc, char *argv[]) {</td>
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1051
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<td class="diff-line-num new_line" data-linenumber="1057" 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">
1057
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="c"> <span class="n" style="color: #333;">genomesubdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Datadir_find_genomesubdir</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fileroot</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">dbversion</span><span class="p">,</span><span class="n" style="color: #333;">user_genomedir</span><span class="p">,</span><span class="n" style="color: #333;">dbroot</span><span class="p">);</span></span>
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1052
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<td class="diff-line-num new_line" data-linenumber="1058" 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">
1058
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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1053" 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">
1053
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<td class="diff-line-num new_line" data-linenumber="1059" 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">
1059
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="1060" 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">
1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transcriptome_dbroot</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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<td class="diff-line-num new new_line" data-linenumber="1061" 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">
1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="c"> <span class="n" style="color: #333;">iitfile</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="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">MALLOC</span><span class="p">((</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">genomesubdir</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1062" 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">
1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="c"> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">fileroot</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">".transcripts/"</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1063" 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">
1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="c"> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">transcriptome_dbroot</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="s" style="color: #d14;">".align.iit"</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1064" 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">
1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">iitfile</span><span class="p">,</span><span class="s" style="color: #d14;">"%s/%s.transcripts/%s.align.iit"</span><span class="p">,</span><span class="n" style="color: #333;">genomesubdir</span><span class="p">,</span><span class="n" style="color: #333;">fileroot</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1065" 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">
1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="c"> <span class="n" style="color: #333;">transcriptome_dbroot</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1066" 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">
1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">map_iit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IIT_read</span><span class="p">(</span><span class="n" style="color: #333;">iitfile</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*name*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*divread*/</span><span class="n" style="color: #333;">READ_ALL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*divstring*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1067" 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">
1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*add_iit_p*/</span><span class="nb" style="color: #0086b3;">true</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 class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1068" 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">
1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span><span class="s" style="color: #d14;">"Cannot open IIT file %s</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;">iitfile</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1069" 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">
1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">9</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1070" 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">
1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IIT_find_one</span><span class="p">(</span><span class="n" style="color: #333;">map_iit</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</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="1071" 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">
1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span><span class="s" style="color: #d14;">"Cannot find %s in map file %s</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;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">iitfile</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1072" 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">
1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1073" 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">
1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="c"> <span class="n" style="color: #333;">annotation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IIT_annotation</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">restofheader</span><span class="p">,</span><span class="n" style="color: #333;">map_iit</span><span class="p">,</span><span class="n" style="color: #333;">index</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">allocp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1074" 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">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">annotation</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1075" 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">
1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allocp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1054" 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="1076" 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">
1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="c"> <span class="n" style="color: #333;">FREE</span><span class="p">(</span><span class="n" style="color: #333;">restofheader</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1077" 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">
1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1078" 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">
1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1079" 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">
1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="1080" 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">
1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="c"> <span class="n" style="color: #333;">IIT_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">map_iit</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1081" 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">
1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="c"> <span class="n" style="color: #333;">FREE</span><span class="p">(</span><span class="n" style="color: #333;">iitfile</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1082" 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">
1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="c"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1083" 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">
1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1084" 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">
1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1085" 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">
1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="c"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1086" 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">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="c"></span>
</pre>
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1054
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<td class="diff-line-num new_line" data-linenumber="1087" 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">
1087
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">user_snpsdir</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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1055
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1088
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<pre style="margin: 0;"> <span id="LC1088" class="line" lang="c"> <span class="n" style="color: #333;">snpsdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genomesubdir</span><span class="p">;</span></span>
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1056
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1089
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/commit/f262b91c3454421731c6c3ccfee1a6754aef795b#d747f527041a6e797f86fcd6f1fcd1562bab24a2"><strong>src/gmap.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: gmap.c 2235<span class="idiff left right">29 2020-11-15 02:34:45</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: gmap.c 2235<span class="idiff left right">99 2020-11-21 04:19:47</span>Z twu $"</span><span class="p">;</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -6508,7 +6508,7 @@ main (int argc, char *argv[]) {</td>
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6508
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6508
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<pre style="margin: 0;"> <span id="LC6508" class="line" lang="c"> <span class="n" style="color: #333;">map_iit</span><span class="p">,</span><span class="n" style="color: #333;">map_divint_crosstable</span><span class="p">,</span><span class="n" style="color: #333;">map_exons_p</span><span class="p">,</span><span class="n" style="color: #333;">map_bothstrands_p</span><span class="p">,</span></span>
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6509
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6509
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<pre style="margin: 0;"> <span id="LC6509" class="line" lang="c"> <span class="n" style="color: #333;">nflanking</span><span class="p">,</span><span class="n" style="color: #333;">print_comment_p</span><span class="p">,</span><span class="n" style="color: #333;">sam_read_group_id</span><span class="p">);</span></span>
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6510
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6510
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<pre style="margin: 0;"> <span id="LC6510" class="line" lang="c"></span>
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6511
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<pre style="margin: 0;">-<span id="LC6511" class="line" lang="c"> <span class="n" style="color: #333;">Inbuffer_setup</span><span class="p">(</span><span class="cm" style="color: #998; font-style: italic;">/*filter_if_both_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff">global_genome</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">global_genomealt</span></span><span class="p">);</span></span>
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6511
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<pre style="margin: 0;">+<span id="LC6511" class="line" lang="c"> <span class="n" style="color: #333;">Inbuffer_setup</span><span class="p">(</span><span class="cm" style="color: #998; font-style: italic;">/*filter_if_both_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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6512
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6512
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<pre style="margin: 0;"> <span id="LC6512" class="line" lang="c"></span>
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6513
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<pre style="margin: 0;"> <span id="LC6513" class="line" lang="c"> <span class="n" style="color: #333;">Outbuffer_setup</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 class="n" style="color: #333;">optind</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span><span class="n" style="color: #333;">any_circular_p</span><span class="p">,</span></span>
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6514
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<pre style="margin: 0;"> <span id="LC6514" class="line" lang="c"> <span class="n" style="color: #333;">nworkers</span><span class="p">,</span><span class="n" style="color: #333;">orderedp</span><span class="p">,</span><span class="n" style="color: #333;">quiet_if_excessive_p</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/commit/f262b91c3454421731c6c3ccfee1a6754aef795b#67480aa11532f910477b929399a61a7147daec47"><strong>src/inbuffer.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: inbuffer.c 2235<span class="idiff left right">11 2020-11-14 15:50:08</span>Z twu $"</span><span class="p">;</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: inbuffer.c 2235<span class="idiff left right">98 2020-11-21 04:19:17</span>Z twu $"</span><span class="p">;</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -37,18 +37,8 @@ static Genome_T global_genomealt;</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Inbuffer_setup</span> <span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">filter_if_both_p_in</span> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef GSNAP</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="p">,</span> <span class="n" style="color: #333;">Genome_T</span> <span class="n" style="color: #333;">genome_in</span><span class="p">,</span> <span class="n" style="color: #333;">Genome_T</span> <span class="n" style="color: #333;">genomealt_in</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Inbuffer_setup</span> <span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">filter_if_both_p_in</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">filter_if_both_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_if_both_p_in</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef GSNAP</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">global_genome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genome_in</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">global_genomealt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genomealt_in</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"></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">@@ -308,7 +298,7 @@ fill_buffer (T this) {</td>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"> <span class="n" style="color: #333;">Sequence_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genomeseq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c"> <span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"inbuffer creating request %d</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;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">requestid</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">nread</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Request_new</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">requestid</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left">global_genome</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">global_genomealt</span></span><span class="p">,</span><span class="n" style="color: #333;">queryseq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">nread</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Request_new</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">requestid</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left">/*genome*/</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff">,</span></span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff">/*genomealt*/</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">,</span><span class="n" style="color: #333;">queryseq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">inputid</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/commit/f262b91c3454421731c6c3ccfee1a6754aef795b#e1e0f0c720a674bf1a10020268eee09c7b9bc9ab"><strong>src/inbuffer.h</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* $Id: inbuffer.h 2235<span class="idiff left right">11 2020-11-14 15:50:08</span>Z twu $ */</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* $Id: inbuffer.h 2235<span class="idiff left right">98 2020-11-21 04:19:17</span>Z twu $ */</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef INBUFFER_INCLUDED</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define INBUFFER_INCLUDED</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</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">@@ -30,11 +30,7 @@</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">T</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Inbuffer_setup</span> <span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">filter_if_both_p_in</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef GSNAP</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"> <span class="p">,</span> <span class="n" style="color: #333;">Genome_T</span> <span class="n" style="color: #333;">genome_in</span><span class="p">,</span> <span class="n" style="color: #333;">Genome_T</span> <span class="n" style="color: #333;">genomealt_in</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Inbuffer_setup</span> <span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">filter_if_both_p_in</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef GSNAP</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">T</span></span>
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