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<h3>
Dylan Aïssi pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/plink1-9">Debian Med / plink1.9</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink1-9/commit/179bb50324fe8f8939714696a3c0e31323b16eb9">179bb503</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-03-08T21:45:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.90~b5.3-180221</pre>
</li>
</ul>
<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">
plink.c
</a>
</li>
<li class="file-stats">
<a href="#f101da6685d6d3284ff66b606e058f55eebde6b7">
plink_data.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">
<a href="https://salsa.debian.org/med-team/plink1-9/commit/179bb50324fe8f8939714696a3c0e31323b16eb9#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb"><strong>plink.c</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="93" 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">@@ -93,7 +93,7 @@</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ver_str</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef STABLE_BUILD</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"> <span class="s" style="color: #d14;">"PLINK v1.90b5.<span class="idiff left right">2</span>"</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"> <span class="s" style="color: #d14;">"PLINK v1.90b5.<span class="idiff left right">3</span>"</span></span>
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="s" style="color: #d14;">"PLINK v1.90p"</span></span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" 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="105" 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">@@ -105,10 +105,10 @@ static const char ver_str[] =</td>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> <span class="s" style="color: #d14;">" 32-bit"</span></span>
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<pre style="margin: 0;"> <span id="LC107" 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="LC108" class="line" lang="c"> <span class="s" style="color: #d14;">" (<span class="idiff left right">9 Jan</span> 2018)"</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="s" style="color: #d14;">" (<span class="idiff left right">21 Feb</span> 2018)"</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ver_str2</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// include leading space if day < 10, so character length stays the same</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"> <span class="s" style="color: #d14;">"<span class="idiff left right"> </span>"</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef STABLE_BUILD</span></span>
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"> <span class="s" style="color: #d14;">" "</span> <span class="c1" style="color: #998; font-style: italic;">// (don't want this when version number has two trailing digits)</span></span>
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<a href="https://salsa.debian.org/med-team/plink1-9/commit/179bb50324fe8f8939714696a3c0e31323b16eb9#f101da6685d6d3284ff66b606e058f55eebde6b7"><strong>plink_data.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16203" 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="16203" 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">@@ -16203,11 +16203,11 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam</td>
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16203
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16203
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<pre style="margin: 0;"> <span id="LC16203" class="line" lang="c"> <span class="p">}</span></span>
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16204
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16204
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<pre style="margin: 0;"> <span id="LC16204" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_dichot_pheno</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="16205" 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">
16205
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<td class="diff-line-num new_line" data-linenumber="16205" 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">
16205
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<pre style="margin: 0;"> <span id="LC16205" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qsort_ext</span><span class="p">(</span><span class="n" style="color: #333;">sample_fids</span><span class="p">,</span> <span class="n" style="color: #333;">tot_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_sample_full_len</span><span class="p">,</span> <span class="n" style="color: #333;">merge_nsort</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">strcmp_natural_deref</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">strcmp_deref</span><span class="p">,</span> <span class="n" style="color: #333;">pheno_c_char</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>
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16206
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<pre style="margin: 0;">-<span id="LC16206" class="line" lang="c"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_NOMEM</span><span class="p">;</span></span>
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16206
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<pre style="margin: 0;">+<span id="LC16206" class="line" lang="c"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_NOMEM</span><span class="p">;</span></span>
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16207
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16207
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<pre style="margin: 0;"> <span id="LC16207" class="line" lang="c"> <span class="p">}</span></span>
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16208
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<td class="diff-line-num new_line" data-linenumber="16208" 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">
16208
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<pre style="margin: 0;"> <span id="LC16208" 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 old_line" data-linenumber="16209" 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">
16209
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16209
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<pre style="margin: 0;"> <span id="LC16209" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qsort_ext</span><span class="p">(</span><span class="n" style="color: #333;">sample_fids</span><span class="p">,</span> <span class="n" style="color: #333;">tot_sample_ct</span><span class="p">,</span> <span class="n" style="color: #333;">max_sample_full_len</span><span class="p">,</span> <span class="n" style="color: #333;">merge_nsort</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">strcmp_natural_deref</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">strcmp_deref</span><span class="p">,</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;">pheno_d</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;">double</span><span class="p">)))</span> <span class="p">{</span></span>
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16210
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<td class="diff-line-num new_line old" data-linenumber="16210" 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="LC16210" class="line" lang="c"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_NOMEM</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="16211" 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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16210
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<pre style="margin: 0;">+<span id="LC16210" class="line" lang="c"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_NOMEM</span><span class="p">;</span></span>
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16211
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16211
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<pre style="margin: 0;"> <span id="LC16211" class="line" lang="c"> <span class="p">}</span></span>
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16212
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<td class="diff-line-num new_line" data-linenumber="16212" 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">
16212
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<pre style="margin: 0;"> <span id="LC16212" class="line" lang="c"> <span class="p">}</span></span>
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16213
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16213
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<pre style="margin: 0;"> <span id="LC16213" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_sort</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">SAMPLE_SORT_FILE</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="16284" 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="16284" 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">@@ -16284,10 +16284,12 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam</td>
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16284
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<td class="diff-line-num new_line" data-linenumber="16284" 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">
16284
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<pre style="margin: 0;"> <span id="LC16284" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">merge_datasets_ret_WRITE_FAIL</span><span class="p">;</span></span>
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16285
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16285
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<pre style="margin: 0;"> <span id="LC16285" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="16286" 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">
16286
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<td class="diff-line-num new_line" data-linenumber="16286" 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">
16286
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<pre style="margin: 0;"> <span id="LC16286" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_dichot_pheno</span><span class="p">)</span> <span class="p">{</span></span>
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16287
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<td class="diff-line-num new_line old" data-linenumber="16287" 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="LC16287" class="line" lang="c"> <span class="n" style="color: #333;">cc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_c_char</span><span class="p">[</span><span class="n" style="color: #333;">ulii</span><span class="p">];</span></span>
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<td class="diff-line-num new old_line" data-linenumber="16288" 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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16287
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<pre style="margin: 0;">+<span id="LC16287" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (21 Feb 2018): need to use the map_reverse index here,</span></span>
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16288
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<pre style="margin: 0;">+<span id="LC16288" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// since the phenotypes correspond to ASCII-sorted sample ID order.</span></span>
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<pre style="margin: 0;">+<span id="LC16289" class="line" lang="c"> <span class="n" style="color: #333;">cc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pheno_c_char</span><span class="p">[</span><span class="n" style="color: #333;">ujj</span><span class="p">];</span></span>
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16288
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16290
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<pre style="margin: 0;"> <span id="LC16290" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%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;">cc</span><span class="o" style="font-weight: 600;">?</span> <span class="p">((</span><span class="n" style="color: #333;">cc</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="s" style="color: #d14;">"2"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"-9"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"1"</span><span class="p">);</span></span>
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16291
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<pre style="margin: 0;"> <span id="LC16291" 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="LC16290" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%g</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;">pheno_d</span><span class="p">[</span><span class="n" style="color: #333;">u<span class="idiff left right">lii</span></span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC16292" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%g</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;">pheno_d</span><span class="p">[</span><span class="n" style="color: #333;">u<span class="idiff left right">jj</span></span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC16293" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC16294" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC16295" class="line" lang="c"> <span class="p">}</span></span>
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