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<h3>
Dylan Aïssi pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/plink2">Debian Med / plink2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plink2/-/commit/478fa15a9c3f8ddd39b3c7a13256f694a14f8cbe">478fa15a</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2021-08-21T09:50:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.00~a3-210816+dfsg</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#6156cd6ac57d8b88e473d9202392ec064b623c93">
LICENSE
→
COPYING
</a>
</li>
<li class="file-stats">
<a href="#68ee82fe07ee986b056119901576b6a2ea827f45">
<span class="new-file">
+
COPYING.LESSER
</span>
</a>
</li>
<li class="file-stats">
<a href="#3e908d19ead2dcc4aa0e25088f26830042de1e7c">
Python/ReadMe.md
</a>
</li>
<li class="file-stats">
<a href="#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f">
plink2.cc
</a>
</li>
<li class="file-stats">
<a href="#82c8c0946825d16815c68e845955a90079d70b6b">
plink2_glm.cc
</a>
</li>
<li class="file-stats">
<a href="#de41b6d72d79193624852ea9511a56681eebfdb2">
plink2_help.cc
</a>
</li>
<li class="file-stats">
<a href="#21274e2b169d6e71a254a974b86ae7af8acdf275">
plink2_import.cc
</a>
</li>
<li class="file-stats">
<a href="#68ec2c295201ac9d061fcfc37744eba392732614">
plink2_misc.cc
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="6156cd6ac57d8b88e473d9202392ec064b623c93">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/478fa15a9c3f8ddd39b3c7a13256f694a14f8cbe#6156cd6ac57d8b88e473d9202392ec064b623c93"><strong>LICENSE</strong>
→
<strong>COPYING</strong>
</a>
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<li id="68ee82fe07ee986b056119901576b6a2ea827f45">
<a href="https://salsa.debian.org/med-team/plink2/-/commit/478fa15a9c3f8ddd39b3c7a13256f694a14f8cbe#68ee82fe07ee986b056119901576b6a2ea827f45"><strong>COPYING.LESSER</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"> GNU LESSER GENERAL PUBLIC LICENSE</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Version 3, 29 June 2007</span>
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3
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Everyone is permitted to copy and distribute verbatim copies</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> of this license document, but changing it is not allowed.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> This version of the GNU Lesser General Public License incorporates</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">the terms and conditions of version 3 of the GNU General Public</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">License, supplemented by the additional permissions listed below.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> 0. Additional Definitions.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> As used herein, "this License" refers to version 3 of the GNU Lesser</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">General Public License, and the "GNU GPL" refers to version 3 of the GNU</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">General Public License.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> "The Library" refers to a covered work governed by this License,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">other than an Application or a Combined Work as defined below.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> An "Application" is any work that makes use of an interface provided</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">by the Library, but which is not otherwise based on the Library.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Defining a subclass of a class defined by the Library is deemed a mode</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">of using an interface provided by the Library.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> A "Combined Work" is a work produced by combining or linking an</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Application with the Library. The particular version of the Library</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">with which the Combined Work was made is also called the "Linked</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Version".</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> The "Minimal Corresponding Source" for a Combined Work means the</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Corresponding Source for the Combined Work, excluding any source code</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">for portions of the Combined Work that, considered in isolation, are</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">based on the Application, and not on the Linked Version.</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> The "Corresponding Application Code" for a Combined Work means the</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">object code and/or source code for the Application, including any data</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">and utility programs needed for reproducing the Combined Work from the</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Application, but excluding the System Libraries of the Combined Work.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> 1. Exception to Section 3 of the GNU GPL.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> You may convey a covered work under sections 3 and 4 of this License</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">without being bound by section 3 of the GNU GPL.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> 2. Conveying Modified Versions.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> If you modify a copy of the Library, and, in your modifications, a</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">facility refers to a function or data to be supplied by an Application</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">that uses the facility (other than as an argument passed when the</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">facility is invoked), then you may convey a copy of the modified</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">version:</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> a) under this License, provided that you make a good faith effort to</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> ensure that, in the event an Application does not supply the</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> function or data, the facility still operates, and performs</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> whatever part of its purpose remains meaningful, or</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> b) under the GNU GPL, with none of the additional permissions of</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> this License applicable to that copy.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> 3. Object Code Incorporating Material from Library Header Files.</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> The object code form of an Application may incorporate material from</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">a header file that is part of the Library. You may convey such object</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">code under terms of your choice, provided that, if the incorporated</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">material is not limited to numerical parameters, data structure</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">layouts and accessors, or small macros, inline functions and templates</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">(ten or fewer lines in length), you do both of the following:</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> a) Give prominent notice with each copy of the object code that the</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> Library is used in it and that the Library and its use are</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> covered by this License.</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> b) Accompany the object code with a copy of the GNU GPL and this license</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> document.</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> 4. Combined Works.</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> You may convey a Combined Work under terms of your choice that,</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">taken together, effectively do not restrict modification of the</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">portions of the Library contained in the Combined Work and reverse</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">engineering for debugging such modifications, if you also do each of</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">the following:</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> a) Give prominent notice with each copy of the Combined Work that</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> the Library is used in it and that the Library and its use are</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> covered by this License.</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> b) Accompany the Combined Work with a copy of the GNU GPL and this license</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> document.</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> c) For a Combined Work that displays copyright notices during</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> execution, include the copyright notice for the Library among</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> these notices, as well as a reference directing the user to the</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> copies of the GNU GPL and this license document.</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> d) Do one of the following:</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> 0) Convey the Minimal Corresponding Source under the terms of this</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> License, and the Corresponding Application Code in a form</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> suitable for, and under terms that permit, the user to</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> recombine or relink the Application with a modified version of</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> the Linked Version to produce a modified Combined Work, in the</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> manner specified by section 6 of the GNU GPL for conveying</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> Corresponding Source.</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> 1) Use a suitable shared library mechanism for linking with the</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> Library. A suitable mechanism is one that (a) uses at run time</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> a copy of the Library already present on the user's computer</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> system, and (b) will operate properly with a modified version</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> of the Library that is interface-compatible with the Linked</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> Version.</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> e) Provide Installation Information, but only if you would otherwise</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> be required to provide such information under section 6 of the</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> GNU GPL, and only to the extent that such information is</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> necessary to install and execute a modified version of the</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> Combined Work produced by recombining or relinking the</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> Application with a modified version of the Linked Version. (If</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> you use option 4d0, the Installation Information must accompany</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> the Minimal Corresponding Source and Corresponding Application</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> Code. If you use option 4d1, you must provide the Installation</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> Information in the manner specified by section 6 of the GNU GPL</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> for conveying Corresponding Source.)</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> 5. Combined Libraries.</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> You may place library facilities that are a work based on the</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">Library side by side in a single library together with other library</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">facilities that are not Applications and are not covered by this</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">License, and convey such a combined library under terms of your</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">choice, if you do both of the following:</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> a) Accompany the combined library with a copy of the same work based</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> on the Library, uncombined with any other library facilities,</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> conveyed under the terms of this License.</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> b) Give prominent notice with the combined library that part of it</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> is a work based on the Library, and explaining where to find the</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> accompanying uncombined form of the same work.</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> 6. Revised Versions of the GNU Lesser General Public License.</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> The Free Software Foundation may publish revised and/or new versions</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">of the GNU Lesser General Public License from time to time. Such new</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">versions will be similar in spirit to the present version, but may</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">differ in detail to address new problems or concerns.</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> Each version is given a distinguishing version number. If the</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">Library as you received it specifies that a certain numbered version</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">of the GNU Lesser General Public License "or any later version"</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">applies to it, you have the option of following the terms and</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">conditions either of that published version or of any later version</span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">published by the Free Software Foundation. If the Library as you</span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">received it does not specify a version number of the GNU Lesser</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">General Public License, you may choose any version of the GNU Lesser</span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">General Public License ever published by the Free Software Foundation.</span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> If the Library as you received it specifies that a proxy can decide</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">whether future versions of the GNU Lesser General Public License shall</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">apply, that proxy's public statement of acceptance of any version is</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">permanent authorization for you to choose that version for the</span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">Library.</span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/478fa15a9c3f8ddd39b3c7a13256f694a14f8cbe#3e908d19ead2dcc4aa0e25088f26830042de1e7c"><strong>Python/ReadMe.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown">This provides a basic Python API for pgenlib; see python_api.txt for details.</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown">This provides a basic Python API for pgenlib (See <span class="p">[</span><span class="nv" style="color: #008080;">python_api.txt</span><span class="p">](</span><span class="sx" style="color: #d14;">python_api.txt</span><span class="p">)</span> for details.)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##### Build this with this.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">Cython and NumPy must be installed.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">python3 setup.py build_ext</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">[sudo] python3 setup.py install</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">```</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##### Example usage:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">#write a 2 sample file</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">import numpy as np</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">import pgenlib as pg</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">with pg.PgenWriter("test.pgen".encode("utf-8"), 2, 3, False) as writer:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"> writer.append_alleles(np.array([0,1,1,1],dtype=np.int32))</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"> writer.append_alleles(np.array([0,1,0,0],dtype=np.int32))</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"> writer.append_alleles(np.array([0,0,0,0],dtype=np.int32))</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">Build this with e.g.</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"> python3 setup.py build_ext</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"> [sudo] python3 setup.py install</span></pre>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">```</span></span></pre>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/478fa15a9c3f8ddd39b3c7a13256f694a14f8cbe#e828d66bb2fc597bda91bc643d9d9d5df9c3de2f"><strong>plink2.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,10 +71,10 @@ static const char ver_str[] = "PLINK v2.00a3"</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="">#ifdef USE_MKL</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang=""> " Intel"</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="">#endif</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang=""> " (1<span class="idiff left right"> Jul</span> 2021)";</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang=""> " (1<span class="idiff left right">6 Aug</span> 2021)";</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="">static const char ver_str2[] =</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang=""> // include leading space if day < 10, so character length stays the same</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang=""> "<span class="idiff left right"> </span>"</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang=""> ""</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="">#ifndef LAPACK_ILP64</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang=""> " "</span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="">#endif</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">@@ -4957,6 +4957,7 @@ BoolErr AllocAndInitReportedTestNames(const uintptr_t* parameter_subset, const c</td>
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4957
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<pre style="margin: 0;"> <span id="LC4957" class="line" lang=""> test_name_buf_iter = iter_next;</span>
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4958
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4958
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<pre style="margin: 0;"> <span id="LC4958" class="line" lang=""> }</span>
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4959
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4959
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<pre style="margin: 0;"> <span id="LC4959" class="line" lang=""> uint32_t pred_uidx = 2 + domdev_present;</span>
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4960
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<pre style="margin: 0;">+<span id="LC4960" class="line" lang=""> // bugfix (16 Aug 2021): sex + interaction?</span>
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4960
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4961
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<pre style="margin: 0;"> <span id="LC4961" class="line" lang=""> for (uint32_t covar_idx = 0; covar_idx != covar_ct; ++covar_idx, ++pred_uidx) {</span>
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4961
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4962
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<pre style="margin: 0;"> <span id="LC4962" class="line" lang=""> if (parameter_subset && (!IsSet(parameter_subset, pred_uidx))) {</span>
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4962
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4963
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<pre style="margin: 0;"> <span id="LC4963" class="line" lang=""> continue;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10910" 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="10911" 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">@@ -10910,9 +10911,10 @@ static const double kSexMaleToCovarD[2] = {2.0, 1.0};</td>
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10910
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10911
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<pre style="margin: 0;"> <span id="LC10911" class="line" lang="">void SexInteractionReshuffle(uint32_t first_interaction_pred_uidx, uint32_t raw_covar_ct, uint32_t domdev_present, uint32_t biallelic_raw_predictor_ctl, uintptr_t* __restrict parameters_or_tests, uintptr_t* __restrict parameter_subset_reshuffle_buf) {</span>
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10911
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10912
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<pre style="margin: 0;"> <span id="LC10912" class="line" lang=""> ZeroWArr(biallelic_raw_predictor_ctl, parameter_subset_reshuffle_buf);</span>
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10912
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10913
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<pre style="margin: 0;"> <span id="LC10913" class="line" lang=""> CopyBitarrRange(parameters_or_tests, 0, 0, first_interaction_pred_uidx - 1, parameter_subset_reshuffle_buf);</span>
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10913
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<td class="new_line diff-line-num old" data-linenumber="10914" 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="LC10913" class="line" lang=""> const uint32_t raw_interaction_ct = raw_covar_ct * (domdev_present + 1);</span>
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10914
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<pre style="margin: 0;">-<span id="LC10914" class="line" lang=""> CopyBitarrRange(parameters_or_tests, first_interaction_pred_uidx - 1, first_interaction_pred_uidx, raw_interaction_ct, parameter_subset_reshuffle_buf);</span>
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10915
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<td class="new_line diff-line-num old" data-linenumber="10914" 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="LC10915" class="line" lang=""> const uint32_t first_sex_parameter_idx = first_interaction_pred_uidx - 1 + raw_interaction_ct;</span>
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<td class="old_line diff-line-num new" data-linenumber="10916" 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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10914
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<pre style="margin: 0;">+<span id="LC10914" class="line" lang=""> // bugfix (16 Aug 2021): raw_covar_ct includes sex</span>
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10915
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<pre style="margin: 0;">+<span id="LC10915" class="line" lang=""> const uint32_t raw_nonsex_interaction_ct = (raw_covar_ct - 1) * (domdev_present + 1);</span>
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10916
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<pre style="margin: 0;">+<span id="LC10916" class="line" lang=""> CopyBitarrRange(parameters_or_tests, first_interaction_pred_uidx - 1, first_interaction_pred_uidx, raw_nonsex_interaction_ct, parameter_subset_reshuffle_buf);</span>
</pre>
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10917
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<pre style="margin: 0;">+<span id="LC10917" class="line" lang=""> const uint32_t first_sex_parameter_idx = first_interaction_pred_uidx - 1 + raw_nonsex_interaction_ct;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10916" 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">
10916
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10918
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<pre style="margin: 0;"> <span id="LC10918" class="line" lang=""> if (IsSet(parameters_or_tests, first_sex_parameter_idx)) {</span>
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10917
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10919
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<pre style="margin: 0;"> <span id="LC10919" class="line" lang=""> SetBit(first_interaction_pred_uidx - 1, parameter_subset_reshuffle_buf);</span>
</pre>
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10918
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10920
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<pre style="margin: 0;"> <span id="LC10920" class="line" lang=""> }</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">@@ -2059,9 +2059,9 @@ PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {</td>
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<pre style="margin: 0;"> <span id="LC2059" class="line" lang="cpp"><span class="s" style="color: #d14;">" otherwise, column 3 is assumed. Use 'col-num=' to force a column number.</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="LC2060" class="line" lang="cpp"><span class="s" style="color: #d14;">" * Only the first character in the sex column is processed. By default,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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2061
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<pre style="margin: 0;"> <span id="LC2061" class="line" lang="cpp"><span class="s" style="color: #d14;">" '1'/'M'/'m' is interpreted as male, '2'/'F'/'f' is interpreted as female,</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="LC2062" class="line" lang="cpp"><span class="s" style="color: #d14;">" and '0'/'N' is interpreted as unknown-sex. To change this to<span class="idiff left right"> '0'/'M'/'m'</span></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="LC2063" class="line" lang="cpp"><span class="s" style="color: #d14;">" = male, '1'/'F'/'f' = female, anything else other than '2' =<span class="idiff left right"> unknown-sex,</span></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="LC2064" class="line" lang="cpp"><span class="s" style="color: #d14;">" add 'male0'.</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="LC2062" class="line" lang="cpp"><span class="s" style="color: #d14;">" and '0'/'N'<span class="idiff left right">/'U'/'u'</span> is interpreted as unknown-sex. To change this to</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="LC2063" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right">'0'/'M'/'m' </span>= male, '1'/'F'/'f' = female, anything else other than '2' =</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="LC2064" class="line" lang="cpp"><span class="s" style="color: #d14;">" <span class="idiff left right">unknown-sex, </span>add 'male0'.</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="LC2065" class="line" lang="cpp"> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2066" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// don't make --real-ref-alleles apply to e.g. Oxford import, since</span></span>
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<pre style="margin: 0;"> <span id="LC2067" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// explicit 'ref-first'/'ref-last' modifiers are clearer</span></span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/478fa15a9c3f8ddd39b3c7a13256f694a14f8cbe#21274e2b169d6e71a254a974b86ae7af8acdf275"><strong>plink2_import.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2935,7 +2935,7 @@ PglErr VcfToPgen(const char* vcfname, const char* preexisting_psamname, const ch</td>
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<pre style="margin: 0;"> <span id="LC2935" class="line" lang=""> }</span>
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<pre style="margin: 0;"> <span id="LC2936" class="line" lang=""> if (unlikely((!sample_ct) && (!no_samples_ok))) {</span>
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<pre style="margin: 0;"> <span id="LC2937" class="line" lang=""> logerrputs("Error: No samples in --vcf file. (This is only permitted when you haven't\nspecified another operation which requires genotype or sample information.)\n");</span>
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<pre style="margin: 0;">-<span id="LC2938" class="line" lang=""> goto VcfToPgen_ret_<span class="idiff left right">INCONSISTENT_INPUT</span>;</span>
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<pre style="margin: 0;">+<span id="LC2938" class="line" lang=""> goto VcfToPgen_ret_<span class="idiff left right">DEGENERATE_DATA</span>;</span>
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<pre style="margin: 0;"> <span id="LC2939" class="line" lang=""> }</span>
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<pre style="margin: 0;"> <span id="LC2940" class="line" lang=""> vic.vibc.sample_ct = sample_ct;</span>
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<pre style="margin: 0;"> <span id="LC2941" class="line" lang=""> // bugfix (5 Jun 2018): must initialize qual_field_ct to zero</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">@@ -3208,7 +3208,7 @@ PglErr VcfToPgen(const char* vcfname, const char* preexisting_psamname, const ch</td>
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3208
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3208
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<pre style="margin: 0;"> <span id="LC3208" class="line" lang=""> }</span>
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3209
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3209
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<pre style="margin: 0;"> <span id="LC3209" class="line" lang=""> } else if (unlikely(!variant_ct)) {</span>
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3210
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3210
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<pre style="margin: 0;"> <span id="LC3210" class="line" lang=""> logerrputs("Error: No variants in --vcf file.\n");</span>
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3211
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<td class="new_line diff-line-num old" data-linenumber="3211" 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="LC3211" class="line" lang=""> goto VcfToPgen_ret_<span class="idiff left right">INCONSISTENT_INPUT</span>;</span>
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3211
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<pre style="margin: 0;">+<span id="LC3211" class="line" lang=""> goto VcfToPgen_ret_<span class="idiff left right">DEGENERATE_DATA</span>;</span>
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3212
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3212
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<pre style="margin: 0;"> <span id="LC3212" class="line" lang=""> }</span>
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3213
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3213
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<pre style="margin: 0;">
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3214
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3214
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<pre style="margin: 0;"> <span id="LC3214" class="line" lang=""> putc_unlocked('\r', stdout);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3875" 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="3875" 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">@@ -3875,6 +3875,9 @@ PglErr VcfToPgen(const char* vcfname, const char* preexisting_psamname, const ch</td>
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3875
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3875
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<pre style="margin: 0;"> <span id="LC3875" class="line" lang=""> VcfToPgen_ret_THREAD_CREATE_FAIL:</span>
</pre>
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3876
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3876
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<pre style="margin: 0;"> <span id="LC3876" class="line" lang=""> reterr = kPglRetThreadCreateFail;</span>
</pre>
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3877
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3877
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<pre style="margin: 0;"> <span id="LC3877" class="line" lang=""> break;</span>
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<td class="old_line diff-line-num new" data-linenumber="3878" 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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3878
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<pre style="margin: 0;">+<span id="LC3878" class="line" lang=""> VcfToPgen_ret_DEGENERATE_DATA:</span>
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<td class="new_line diff-line-num new" data-linenumber="3879" 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">
3879
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<pre style="margin: 0;">+<span id="LC3879" class="line" lang=""> reterr = kPglRetDegenerateData;</span>
</pre>
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3880
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<pre style="margin: 0;">+<span id="LC3880" class="line" lang=""> break;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="3878" 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">
3878
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3881
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<pre style="margin: 0;"> <span id="LC3881" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="3879" 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">
3879
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<td class="new_line diff-line-num" data-linenumber="3882" 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">
3882
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<pre style="margin: 0;"> <span id="LC3882" class="line" lang=""> VcfToPgen_ret_1:</span>
</pre>
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3880
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<td class="new_line diff-line-num" data-linenumber="3883" 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">
3883
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<pre style="margin: 0;"> <span id="LC3883" class="line" lang=""> CleanupSpgw(&spgw, &reterr);</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7352" 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="7355" 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">@@ -7352,7 +7355,7 @@ PglErr BcfToPgen(const char* bcfname, const char* preexisting_psamname, const ch</td>
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7352
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7355
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<pre style="margin: 0;"> <span id="LC7355" class="line" lang=""> }</span>
</pre>
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7353
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<td class="new_line diff-line-num" data-linenumber="7356" 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">
7356
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<pre style="margin: 0;"> <span id="LC7356" class="line" lang=""> if (unlikely((!sample_ct) && (!no_samples_ok))) {</span>
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<td class="old_line diff-line-num" data-linenumber="7354" 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">
7354
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<td class="new_line diff-line-num" data-linenumber="7357" 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">
7357
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7357" class="line" lang=""> logerrputs("Error: No samples in BCF text header block. (This is only permitted when you\nhaven't specified another operation which requires genotype or sample\ninformation.)\n");</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7355" 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">
7355
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<td class="new_line diff-line-num old" data-linenumber="7358" 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">
</td>
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<pre style="margin: 0;">-<span id="LC7355" class="line" lang=""> goto BcfToPgen_ret_<span class="idiff left right">INCONSISTENT_INPUT</span>;</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="7358" 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">
7358
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<pre style="margin: 0;">+<span id="LC7358" class="line" lang=""> goto BcfToPgen_ret_<span class="idiff left right">DEGENERATE_DATA</span>;</span>
</pre>
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7356
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<td class="new_line diff-line-num" data-linenumber="7359" 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">
7359
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<pre style="margin: 0;"> <span id="LC7359" class="line" lang=""> }</span>
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7357
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7360
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<pre style="margin: 0;"> <span id="LC7360" class="line" lang=""> if (unlikely(sample_ct >= (1 << 24))) {</span>
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7358
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7361
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<pre style="margin: 0;"> <span id="LC7361" class="line" lang=""> snprintf(g_logbuf, kLogbufSize, "Error: BCF text header block has %u sample IDs, which is larger than the BCF limit of 2^24 - 1.\n", sample_ct);</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8012" 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="8015" 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">@@ -8012,7 +8015,7 @@ PglErr BcfToPgen(const char* bcfname, const char* preexisting_psamname, const ch</td>
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8012
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8015
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<pre style="margin: 0;"> <span id="LC8015" class="line" lang=""> }</span>
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8013
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<td class="new_line diff-line-num" data-linenumber="8016" 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">
8016
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<pre style="margin: 0;"> <span id="LC8016" class="line" lang=""> } else if (unlikely(!variant_ct)) {</span>
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8014
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8017
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<pre style="margin: 0;"> <span id="LC8017" class="line" lang=""> logerrputs("Error: No variants in --bcf file.\n");</span>
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8015
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<pre style="margin: 0;">-<span id="LC8015" class="line" lang=""> goto BcfToPgen_ret_<span class="idiff left right">INCONSISTENT_INPUT</span>;</span>
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8018
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<pre style="margin: 0;">+<span id="LC8018" class="line" lang=""> goto BcfToPgen_ret_<span class="idiff left right">DEGENERATE_DATA</span>;</span>
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8016
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8019
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<pre style="margin: 0;"> <span id="LC8019" class="line" lang=""> }</span>
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8017
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8020
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<pre style="margin: 0;">
</pre>
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8018
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8021
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<pre style="margin: 0;"> <span id="LC8021" class="line" lang=""> const uintptr_t variant_skip_ct = vrec_idx - 1 - variant_ct;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8983" 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="8986" 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">@@ -8983,6 +8986,9 @@ PglErr BcfToPgen(const char* bcfname, const char* preexisting_psamname, const ch</td>
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8983
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8986
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<pre style="margin: 0;"> <span id="LC8986" class="line" lang=""> BcfToPgen_ret_THREAD_CREATE_FAIL:</span>
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8984
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8987
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<pre style="margin: 0;"> <span id="LC8987" class="line" lang=""> reterr = kPglRetThreadCreateFail;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="8985" 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">
8985
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8988
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<pre style="margin: 0;"> <span id="LC8988" class="line" lang=""> break;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="8986" 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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8989
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<pre style="margin: 0;">+<span id="LC8989" class="line" lang=""> BcfToPgen_ret_DEGENERATE_DATA:</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="8990" 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">
8990
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<pre style="margin: 0;">+<span id="LC8990" class="line" lang=""> reterr = kPglRetDegenerateData;</span>
</pre>
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8991
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<pre style="margin: 0;">+<span id="LC8991" class="line" lang=""> break;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="8986" 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">
8986
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8992
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<pre style="margin: 0;"> <span id="LC8992" class="line" lang=""> }</span>
</pre>
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8987
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8993
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8993" class="line" lang=""> BcfToPgen_ret_1:</span>
</pre>
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8988
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<td class="new_line diff-line-num" data-linenumber="8994" 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">
8994
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<pre style="margin: 0;"> <span id="LC8994" class="line" lang=""> CleanupSpgw(&spgw, &reterr);</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9387" 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="9393" 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">@@ -9387,7 +9393,7 @@ PglErr OxSampleToPsam(const char* samplename, const char* const_fid, const char*</td>
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<td class="old_line diff-line-num" data-linenumber="9387" 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">
9387
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9393
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<pre style="margin: 0;"> <span id="LC9393" class="line" lang=""> const uint32_t sample_ct = line_idx - 3;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9388" 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">
9388
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<td class="new_line diff-line-num" data-linenumber="9394" 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">
9394
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<pre style="margin: 0;"> <span id="LC9394" class="line" lang=""> if (unlikely(!sample_ct)) {</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9389" 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">
9389
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<td class="new_line diff-line-num" data-linenumber="9395" 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">
9395
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9395" class="line" lang=""> logerrputs("Error: No samples in .sample file.\n");</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="9390" 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">
9390
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<td class="new_line diff-line-num old" data-linenumber="9396" 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="LC9390" class="line" lang=""> goto OxSampleToPsam_ret_<span class="idiff left right">INCONSISTENT_INPUT</span>;</span>
</pre>
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9396
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<pre style="margin: 0;">+<span id="LC9396" class="line" lang=""> goto OxSampleToPsam_ret_<span class="idiff left right">DEGENERATE_DATA</span>;</span>
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9391
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9397
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<pre style="margin: 0;"> <span id="LC9397" class="line" lang=""> }</span>
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9392
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9398
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<pre style="margin: 0;"> <span id="LC9398" class="line" lang=""> const char* all_ids_iter = all_ids_start;</span>
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9393
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9399
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<pre style="margin: 0;"> <span id="LC9399" class="line" lang=""> uint32_t nz_fid_present = 0;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9695" 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="9701" 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">@@ -9695,6 +9701,9 @@ PglErr OxSampleToPsam(const char* samplename, const char* const_fid, const char*</td>
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9695
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<td class="new_line diff-line-num" data-linenumber="9701" 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">
9701
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<pre style="margin: 0;"> <span id="LC9701" class="line" lang=""> OxSampleToPsam_ret_INCONSISTENT_INPUT:</span>
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9696
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<td class="new_line diff-line-num" data-linenumber="9702" 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">
9702
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<pre style="margin: 0;"> <span id="LC9702" class="line" lang=""> reterr = kPglRetInconsistentInput;</span>
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<td class="old_line diff-line-num" data-linenumber="9697" 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">
9697
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<td class="new_line diff-line-num" data-linenumber="9703" 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">
9703
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<pre style="margin: 0;"> <span id="LC9703" class="line" lang=""> break;</span>
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9704
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<pre style="margin: 0;">+<span id="LC9704" class="line" lang=""> OxSampleToPsam_ret_DEGENERATE_DATA:</span>
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<td class="new_line diff-line-num new" data-linenumber="9705" 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">
9705
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<pre style="margin: 0;">+<span id="LC9705" class="line" lang=""> reterr = kPglRetDegenerateData;</span>
</pre>
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9706
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<pre style="margin: 0;">+<span id="LC9706" class="line" lang=""> break;</span>
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9698
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9707
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<pre style="margin: 0;"> <span id="LC9707" class="line" lang=""> }</span>
</pre>
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9699
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9708
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<pre style="margin: 0;"> <span id="LC9708" class="line" lang=""> OxSampleToPsam_ret_1:</span>
</pre>
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9700
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9709
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<pre style="margin: 0;"> <span id="LC9709" class="line" lang=""> CleanupTextStream2(".sample file", &sample_txs, &reterr);</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9896" 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="9905" 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">@@ -9896,7 +9905,7 @@ PglErr OxGenToPgen(const char* genname, const char* samplename, const char* cons</td>
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<td class="old_line diff-line-num" data-linenumber="9896" 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">
9896
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<td class="new_line diff-line-num" data-linenumber="9905" 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">
9905
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<pre style="margin: 0;"> <span id="LC9905" class="line" lang=""> goto OxGenToPgen_ret_TSTREAM_FAIL;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9897" 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">
9897
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<td class="new_line diff-line-num" data-linenumber="9906" 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">
9906
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<pre style="margin: 0;"> <span id="LC9906" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9898" 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">
9898
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<td class="new_line diff-line-num" data-linenumber="9907" 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">
9907
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<pre style="margin: 0;"> <span id="LC9907" class="line" lang=""> logerrputs("Error: Empty .gen file.\n");</span>
</pre>
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9899
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<td class="new_line diff-line-num old" data-linenumber="9908" 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="LC9899" class="line" lang=""> goto OxGenToPgen_ret_<span class="idiff left right">INCONSISTENT_INPUT</span>;</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="9908" 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">
9908
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<pre style="margin: 0;">+<span id="LC9908" class="line" lang=""> goto OxGenToPgen_ret_<span class="idiff left right">DEGENERATE_DATA</span>;</span>
</pre>
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9900
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<td class="new_line diff-line-num" data-linenumber="9909" 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">
9909
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9909" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9901" 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">
9901
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<td class="new_line diff-line-num" data-linenumber="9910" 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">
9910
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<pre style="margin: 0;"> <span id="LC9910" class="line" lang=""> uint32_t is_v2 = 0;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9902" 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">
9902
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<td class="new_line diff-line-num" data-linenumber="9911" 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">
9911
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<pre style="margin: 0;"> <span id="LC9911" class="line" lang=""> {</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10327" 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="10336" 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">@@ -10327,6 +10336,9 @@ PglErr OxGenToPgen(const char* genname, const char* samplename, const char* cons</td>
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<td class="old_line diff-line-num" data-linenumber="10327" 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">
10327
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<td class="new_line diff-line-num" data-linenumber="10336" 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">
10336
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10336" class="line" lang=""> OxGenToPgen_ret_INCONSISTENT_INPUT:</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10328" 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">
10328
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<td class="new_line diff-line-num" data-linenumber="10337" 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">
10337
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10337" class="line" lang=""> reterr = kPglRetInconsistentInput;</span>
</pre>
</td>
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10329
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10338
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<pre style="margin: 0;"> <span id="LC10338" class="line" lang=""> break;</span>
</pre>
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10339
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<pre style="margin: 0;">+<span id="LC10339" class="line" lang=""> OxGenToPgen_ret_DEGENERATE_DATA:</span>
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<td class="new_line diff-line-num new" data-linenumber="10340" 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">
10340
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<pre style="margin: 0;">+<span id="LC10340" class="line" lang=""> reterr = kPglRetDegenerateData;</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="10341" 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">
10341
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<pre style="margin: 0;">+<span id="LC10341" class="line" lang=""> break;</span>
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<td class="old_line diff-line-num" data-linenumber="10330" 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">
10330
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<td class="new_line diff-line-num" data-linenumber="10342" 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">
10342
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<pre style="margin: 0;"> <span id="LC10342" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10331" 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">
10331
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<td class="new_line diff-line-num" data-linenumber="10343" 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">
10343
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<pre style="margin: 0;"> <span id="LC10343" class="line" lang=""> OxGenToPgen_ret_1:</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10332" 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">
10332
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<td class="new_line diff-line-num" data-linenumber="10344" 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">
10344
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<pre style="margin: 0;"> <span id="LC10344" class="line" lang=""> CleanupSpgw(&spgw, &reterr);</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11820" 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="11832" 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">@@ -11820,7 +11832,7 @@ PglErr OxBgenToPgen(const char* bgenname, const char* samplename, const char* co</td>
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<td class="old_line diff-line-num" data-linenumber="11820" 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">
11820
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<td class="new_line diff-line-num" data-linenumber="11832" 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">
11832
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<pre style="margin: 0;"> <span id="LC11832" class="line" lang=""> const uint32_t raw_variant_ct = initial_uints[2];</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="11821" 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">
11821
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<td class="new_line diff-line-num" data-linenumber="11833" 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">
11833
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<pre style="margin: 0;"> <span id="LC11833" class="line" lang=""> if (unlikely(!raw_variant_ct)) {</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="11822" 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">
11822
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<td class="new_line diff-line-num" data-linenumber="11834" 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">
11834
</td>
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<pre style="margin: 0;"> <span id="LC11834" class="line" lang=""> logerrputs("Error: Empty .bgen file.\n");</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="11823" 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">
11823
</td>
<td class="new_line diff-line-num old" data-linenumber="11835" 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="LC11823" class="line" lang=""> goto OxBgenToPgen_ret_<span class="idiff left right">INCONSISTENT_INPUT</span>;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="11824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="11835" 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">
11835
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<pre style="margin: 0;">+<span id="LC11835" class="line" lang=""> goto OxBgenToPgen_ret_<span class="idiff left right">DEGENERATE_DATA</span>;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="11824" 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">
11824
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<td class="new_line diff-line-num" data-linenumber="11836" 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">
11836
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<pre style="margin: 0;"> <span id="LC11836" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="11825" 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">
11825
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<td class="new_line diff-line-num" data-linenumber="11837" 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">
11837
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<pre style="margin: 0;">
</pre>
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<td class="old_line diff-line-num" data-linenumber="11826" 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">
11826
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<td class="new_line diff-line-num" data-linenumber="11838" 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">
11838
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11838" class="line" lang=""> if (unlikely(fseeko(bgenfile, initial_uints[1], SEEK_SET))) {</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13688" 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="13700" 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">@@ -13688,6 +13700,9 @@ PglErr OxBgenToPgen(const char* bgenname, const char* samplename, const char* co</td>
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<td class="old_line diff-line-num" data-linenumber="13688" 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">
13688
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<td class="new_line diff-line-num" data-linenumber="13700" 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">
13700
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13700" class="line" lang=""> OxBgenToPgen_ret_THREAD_CREATE_FAIL:</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="13689" 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">
13689
</td>
<td class="new_line diff-line-num" data-linenumber="13701" 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">
13701
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13701" class="line" lang=""> reterr = kPglRetThreadCreateFail;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="13690" 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">
13690
</td>
<td class="new_line diff-line-num" data-linenumber="13702" 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">
13702
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13702" class="line" lang=""> break;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="13691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="13703" 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">
13703
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<pre style="margin: 0;">+<span id="LC13703" class="line" lang=""> OxBgenToPgen_ret_DEGENERATE_DATA:</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="13691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="13704" 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">
13704
</td>
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<pre style="margin: 0;">+<span id="LC13704" class="line" lang=""> reterr = kPglRetDegenerateData;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="13691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="13705" 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">
13705
</td>
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<pre style="margin: 0;">+<span id="LC13705" class="line" lang=""> break;</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="13691" 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">
13691
</td>
<td class="new_line diff-line-num" data-linenumber="13706" 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">
13706
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13706" class="line" lang=""> OxBgenToPgen_ret_bgen13_thread_fail:</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="13692" 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">
13692
</td>
<td class="new_line diff-line-num" data-linenumber="13707" 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">
13707
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13707" class="line" lang=""> if (reterr == kPglRetMalformedInput) {</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="13693" 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">
13693
</td>
<td class="new_line diff-line-num" data-linenumber="13708" 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">
13708
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13708" class="line" lang=""> OxBgenToPgen_ret_bgen11_thread_fail:</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14474" 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="14489" 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">@@ -14474,7 +14489,7 @@ PglErr LoadMap(const char* mapname, MiscFlags misc_flags, ChrInfo* cip, uint32_t</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14474" 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">
14474
</td>
<td class="new_line diff-line-num" data-linenumber="14489" 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">
14489
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14489" class="line" lang=""> if (unlikely(!line_start)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14475" 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">
14475
</td>
<td class="new_line diff-line-num" data-linenumber="14490" 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">
14490
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14490" class="line" lang=""> if (!TextStreamErrcode2(&map_txs, &reterr)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14476" 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">
14476
</td>
<td class="new_line diff-line-num" data-linenumber="14491" 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">
14491
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14491" class="line" lang=""> logerrputs("Error: Empty .map file.\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="14477" 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">
14477
</td>
<td class="new_line diff-line-num old" data-linenumber="14492" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC14477" class="line" lang=""> goto LoadMap_ret_<span class="idiff left right">INCONSISTENT_INPUT</span>;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="14478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="14492" 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">
14492
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14492" class="line" lang=""> goto LoadMap_ret_<span class="idiff left right">DEGENERATE_DATA</span>;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14478" 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">
14478
</td>
<td class="new_line diff-line-num" data-linenumber="14493" 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">
14493
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14493" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14479" 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">
14479
</td>
<td class="new_line diff-line-num" data-linenumber="14494" 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">
14494
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14494" class="line" lang=""> goto LoadMap_ret_TSTREAM_FAIL;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14480" 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">
14480
</td>
<td class="new_line diff-line-num" data-linenumber="14495" 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">
14495
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14495" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14687" 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="14702" 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">@@ -14687,6 +14702,9 @@ PglErr LoadMap(const char* mapname, MiscFlags misc_flags, ChrInfo* cip, uint32_t</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14687" 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">
14687
</td>
<td class="new_line diff-line-num" data-linenumber="14702" 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">
14702
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14702" class="line" lang=""> LoadMap_ret_INCONSISTENT_INPUT:</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14688" 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">
14688
</td>
<td class="new_line diff-line-num" data-linenumber="14703" 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">
14703
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14703" class="line" lang=""> reterr = kPglRetInconsistentInput;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14689" 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">
14689
</td>
<td class="new_line diff-line-num" data-linenumber="14704" 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">
14704
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14704" class="line" lang=""> break;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="14690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="14705" 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">
14705
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14705" class="line" lang=""> LoadMap_ret_DEGENERATE_DATA:</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="14690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="14706" 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">
14706
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14706" class="line" lang=""> reterr = kPglRetDegenerateData;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="14690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="14707" 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">
14707
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14707" class="line" lang=""> break;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14690" 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">
14690
</td>
<td class="new_line diff-line-num" data-linenumber="14708" 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">
14708
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14708" class="line" lang=""> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14691" 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">
14691
</td>
<td class="new_line diff-line-num" data-linenumber="14709" 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">
14709
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14709" class="line" lang=""> LoadMap_ret_1:</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="14692" 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">
14692
</td>
<td class="new_line diff-line-num" data-linenumber="14710" 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">
14710
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14710" class="line" lang=""> // ForgetExtraChrNames(1, cip);</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15305" 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="15323" 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">@@ -15305,7 +15323,7 @@ PglErr Plink1DosageToPgen(const char* dosagename, const char* famname, const cha</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="15305" 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">
15305
</td>
<td class="new_line diff-line-num" data-linenumber="15323" 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">
15323
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15323" class="line" lang=""> if (unlikely(!variant_ct)) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="15306" 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">
15306
</td>
<td class="new_line diff-line-num" data-linenumber="15324" 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">
15324
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15324" class="line" lang=""> if (!variant_skip_ct) {</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="15307" 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">
15307
</td>
<td class="new_line diff-line-num" data-linenumber="15325" 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">
15325
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15325" class="line" lang=""> logerrputs("Error: Empty --import-dosage file.\n");</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="15308" 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">
15308
</td>
<td class="new_line diff-line-num old" data-linenumber="15326" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC15308" class="line" lang=""> goto Plink1DosageToPgen_ret_<span class="idiff left right">INCONSISTENT_INPUT</span>;</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="15309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="15326" 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">
15326
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15326" class="line" lang=""> goto Plink1DosageToPgen_ret_<span class="idiff left right">DEGENERATE_DATA</span>;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="15309" 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">
15309
</td>
<td class="new_line diff-line-num" data-linenumber="15327" 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">
15327
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15327" class="line" lang=""> }</span>
</pre>
</td>
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15310
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15328
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<pre style="margin: 0;"> <span id="LC15328" class="line" lang=""> logerrprintfww("Error: All %" PRIuPTR " variant%s in --import-dosage file skipped.\n", variant_skip_ct, (variant_skip_ct == 1)? "" : "s");</span>
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15311
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15329
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<pre style="margin: 0;"> <span id="LC15329" class="line" lang=""> goto Plink1DosageToPgen_ret_INCONSISTENT_INPUT;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15604" 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="15622" 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">@@ -15604,6 +15622,9 @@ PglErr Plink1DosageToPgen(const char* dosagename, const char* famname, const cha</td>
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15604
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15622
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<pre style="margin: 0;"> <span id="LC15622" class="line" lang=""> Plink1DosageToPgen_ret_INCONSISTENT_INPUT:</span>
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15605
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15623
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<pre style="margin: 0;"> <span id="LC15623" class="line" lang=""> reterr = kPglRetInconsistentInput;</span>
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15606
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15624
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<pre style="margin: 0;"> <span id="LC15624" class="line" lang=""> break;</span>
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15625
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<pre style="margin: 0;">+<span id="LC15625" class="line" lang=""> Plink1DosageToPgen_ret_DEGENERATE_DATA:</span>
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15626
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<pre style="margin: 0;">+<span id="LC15626" class="line" lang=""> reterr = kPglRetDegenerateData;</span>
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15627
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<pre style="margin: 0;">+<span id="LC15627" class="line" lang=""> break;</span>
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15628
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<pre style="margin: 0;"> <span id="LC15628" class="line" lang=""> }</span>
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15608
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15629
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<pre style="margin: 0;"> <span id="LC15629" class="line" lang=""> Plink1DosageToPgen_ret_1:</span>
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15609
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15630
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<pre style="margin: 0;"> <span id="LC15630" class="line" lang=""> CleanupSpgw(&spgw, &reterr);</span>
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<a href="https://salsa.debian.org/med-team/plink2/-/commit/478fa15a9c3f8ddd39b3c7a13256f694a14f8cbe#68ec2c295201ac9d061fcfc37744eba392732614"><strong>plink2_misc.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2307,10 +2307,12 @@ PglErr UpdateSampleSexes(const uintptr_t* sample_include, const SampleIdInfo* si</td>
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2307
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<pre style="margin: 0;"> <span id="LC2307" class="line" lang="cpp"> <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;">ujj</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">70</span><span class="p">)</span> <span class="p">{</span></span>
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2308
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2308
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<pre style="margin: 0;"> <span id="LC2308" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 'F'/'f'</span></span>
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2309
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2309
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<pre style="margin: 0;"> <span id="LC2309" class="line" lang="cpp"> <span class="n" style="color: #333;">sexval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2310
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<pre style="margin: 0;">-<span id="LC2310" class="line" lang="cpp"> <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;">unlikely</span><span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">male0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">sexval</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">30</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2310" class="line" lang="cpp"> <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;">unlikely</span><span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">male0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">sexval</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">30</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ujj</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">85</span></span><span class="p"><span class="idiff right">)</span>))</span> <span class="p">{</span></span>
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2311
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<pre style="margin: 0;"> <span id="LC2311" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// allow 'N' = missing to make 1/2/NA work</span></span>
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2312
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<pre style="margin: 0;">+<span id="LC2312" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// allow 'U'/'u' since this is actually being used by Illumina</span></span>
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2313
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<pre style="margin: 0;">+<span id="LC2313" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// GenCall and Affymetrix APT</span></span>
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2312
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2314
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<pre style="margin: 0;"> <span id="LC2314" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// don't permit 'n' for now</span></span>
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<pre style="margin: 0;">-<span id="LC2313" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="n" style="color: #333;">kLogbufSize</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: Invalid sex value on line %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" of --update-sex file. (Acceptable values: 1/M/m = male, 2/F/f = female, 0/N = missing.)</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;">line_idx</span><span class="p">);</span></span>
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2315
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<pre style="margin: 0;">+<span id="LC2315" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">g_logbuf</span><span class="p">,</span> <span class="n" style="color: #333;">kLogbufSize</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: Invalid sex value on line %"</span> <span class="n" style="color: #333;">PRIuPTR</span> <span class="s" style="color: #d14;">" of --update-sex file. (Acceptable values: 1/M/m = male, 2/F/f = female, 0/N<span class="idiff left right">/U</span> = missing.)</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;">line_idx</span><span class="p">);</span></span>
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2314
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2316
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<pre style="margin: 0;"> <span id="LC2316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">UpdateSampleSexes_ret_MALFORMED_INPUT_WW</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2317" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2316
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<pre style="margin: 0;"> <span id="LC2318" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// with 'male0', everything else is treated as missing</span></span>
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