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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/vcftools">Debian Med / vcftools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcftools/commit/99c96e52d046db580495e88bde6083d63e641040">99c96e52</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T13:56:17Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.1.16</pre>
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#4a2fdb4f8510cdbc9a74ea869ad5dfcb7cb32b30">
.tarball-version
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#21e0fb078afe81c84467dde159fdcb0dbfe6dff1">
src/cpp/header.cpp
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<li class="file-stats">
<a href="#70a51bbb550d4d9cde191716b12e8b65bf4701fa">
src/cpp/variant_file_output.cpp
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<li class="file-stats">
<a href="#40503531ecd7b3e02bd10cfd1a817dd199f68795">
src/cpp/vcftools.1
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<li class="file-stats">
<a href="#054442b8ef7093877e9e3cdb4f96a34eb4f6918e">
src/perl/FaSlice.pm
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<li class="file-stats">
<a href="#02d15e2306b36f34d0287e5b446a7447ecaa2027">
src/perl/Vcf.pm
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<li class="file-stats">
<a href="#3d2697ef3bf18ced3cb8b5ac37ba393e1e4e8895">
src/perl/vcf-haplotypes
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<h4>Changes:</h4>
<li id="4a2fdb4f8510cdbc9a74ea869ad5dfcb7cb32b30">
<a href="https://salsa.debian.org/med-team/vcftools/commit/99c96e52d046db580495e88bde6083d63e641040#4a2fdb4f8510cdbc9a74ea869ad5dfcb7cb32b30"><strong>.tarball-version</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">0.1.1<span class="idiff left right">5</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">0.1.1<span class="idiff left right">6</span></span></pre>
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<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/vcftools/commit/99c96e52d046db580495e88bde6083d63e641040#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" 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="74" 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">@@ -74,7 +74,7 @@ AC_ARG_ENABLE([pca],</td>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> [pca=no])</span>
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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">AS_IF([test "x$pca" = "xyes"],[</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> AC_<span class="idiff left right">SEARCH_LIBS([dgeev_], [lapack</span>])</span>
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<td class="diff-line-num new old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> AC_<span class="idiff left right">CHECK_LIB([lapack], [dgeev_</span>])</span>
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<td class="diff-line-num old_line" data-linenumber="78" 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">
78
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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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<td class="diff-line-num old_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"># Generate output.</span>
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<li id="21e0fb078afe81c84467dde159fdcb0dbfe6dff1">
<a href="https://salsa.debian.org/med-team/vcftools/commit/99c96e52d046db580495e88bde6083d63e641040#21e0fb078afe81c84467dde159fdcb0dbfe6dff1"><strong>src/cpp/header.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" 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="110" 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">@@ -110,7 +110,6 @@ int header::add_INFO_descriptor(const string &in, int index)</td>
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<td class="diff-line-num old_line" data-linenumber="110" 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">
110
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">I</span><span class="p">.</span><span class="n" style="color: #333;">Field</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"INFO"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="111" 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">
111
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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tokens</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="112" 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">
112
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<td class="diff-line-num new_line" data-linenumber="112" 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">
112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">details</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">,</span> <span class="n" style="color: #333;">tokens</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Expected at least 4 parts in INFO definition: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" 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="117" 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">@@ -118,7 +117,11 @@ int header::add_INFO_descriptor(const string &in, int index)</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="p">{</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">[</span><span class="n" style="color: #333;">ui</span><span class="p">],</span> <span class="sc" style="color: #d14;">'='</span><span class="p">,</span> <span class="n" style="color: #333;">entry</span><span class="p">);</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="p">{</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: Expected at least 2 parts in INFO entry: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="p">}</span></span>
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122
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ID"</span><span class="p">)</span> <span class="n" style="color: #333;">I</span><span class="p">.</span><span class="n" style="color: #333;">ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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123
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">)</span></span>
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="205" 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="208" 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">@@ -205,7 +208,6 @@ int header::add_FORMAT_descriptor(const string &in, int index)</td>
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205
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">details</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">,</span> <span class="n" style="color: #333;">tokens</span><span class="p">);</span></span>
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206
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">Field_description</span> <span class="n" style="color: #333;">I</span><span class="p">;</span></span>
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207
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">I</span><span class="p">.</span><span class="n" style="color: #333;">Field</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"FORMAT"</span><span class="p">;</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"></span>
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209
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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210
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<td class="diff-line-num new_line" data-linenumber="212" 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">
212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Expected at least 4 parts in FORMAT definition: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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211
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" 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="215" 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">@@ -213,6 +215,11 @@ int header::add_FORMAT_descriptor(const string &in, int index)</td>
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213
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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214
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"> <span class="p">{</span></span>
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215
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">[</span><span class="n" style="color: #333;">ui</span><span class="p">],</span> <span class="sc" style="color: #d14;">'='</span><span class="p">,</span> <span class="n" style="color: #333;">entry</span><span class="p">);</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="p">{</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: Expected at least 2 parts in FORMAT entry: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="p">}</span></span>
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216
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ID"</span><span class="p">)</span> <span class="n" style="color: #333;">I</span><span class="p">.</span><span class="n" style="color: #333;">ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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217
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Number"</span><span class="p">)</span></span>
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218
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="303" 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="310" 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">@@ -303,6 +310,11 @@ void header::add_CONTIG_descriptor(const string &in, int index)</td>
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303
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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304
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="p">{</span></span>
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305
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">[</span><span class="n" style="color: #333;">ui</span><span class="p">],</span> <span class="sc" style="color: #d14;">'='</span><span class="p">,</span> <span class="n" style="color: #333;">entry</span><span class="p">);</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="p">{</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: Expected at least 2 parts in CONTIG entry: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="p">}</span></span>
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306
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ID"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp"> <span class="p">{</span></span>
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308
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">I</span><span class="p">.</span><span class="n" style="color: #333;">ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="354" 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">@@ -342,6 +354,11 @@ int header::add_FILTER_descriptor(const string &in, int index)</td>
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342
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">ui</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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343
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp"> <span class="p">{</span></span>
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344
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">[</span><span class="n" style="color: #333;">ui</span><span class="p">],</span> <span class="sc" style="color: #d14;">'='</span><span class="p">,</span> <span class="n" style="color: #333;">entry</span><span class="p">);</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="p">{</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: Expected at least 2 parts in FORMAT entry: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="p">}</span></span>
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345
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ID"</span><span class="p">)</span> <span class="n" style="color: #333;">I</span><span class="p">.</span><span class="n" style="color: #333;">ID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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346
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">entry</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Description"</span><span class="p">)</span></span>
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347
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="cpp"> <span class="p">{</span></span>
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<li id="70a51bbb550d4d9cde191716b12e8b65bf4701fa">
<a href="https://salsa.debian.org/med-team/vcftools/commit/99c96e52d046db580495e88bde6083d63e641040#70a51bbb550d4d9cde191716b12e8b65bf4701fa"><strong>src/cpp/variant_file_output.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4287" 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>
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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">@@ -4287,8 +4287,10 @@ void variant_file::output_removed_sites(const parameters ¶ms)</td>
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4287
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4287
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<pre style="margin: 0;"> <span id="LC4287" class="line" lang="cpp"> <span class="n" style="color: #333;">N_entries</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">apply_filters</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">);</span></span>
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4288
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4288
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<pre style="margin: 0;"> <span id="LC4288" class="line" lang="cpp"></span>
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4289
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4289
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<pre style="margin: 0;"> <span id="LC4289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">passed_filters</span><span class="p">)</span></span>
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4290
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<pre style="margin: 0;">+<span id="LC4290" class="line" lang="cpp"> <span class="p">{</span></span>
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4291
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<pre style="margin: 0;">+<span id="LC4291" class="line" lang="cpp"> <span class="n" style="color: #333;">N_kept_entries</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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4290
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4292
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<pre style="margin: 0;"> <span id="LC4292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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4291
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<pre style="margin: 0;">-<span id="LC4291" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">N_kept_entries</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff right">;</span></span></span>
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4293
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<pre style="margin: 0;">+<span id="LC4293" class="line" lang="cpp"> <span class="p"><span class="idiff left right">}</span></span></span>
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4292
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4294
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<pre style="margin: 0;"> <span id="LC4294" class="line" lang="cpp"></span>
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4293
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4295
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<pre style="margin: 0;"> <span id="LC4295" class="line" lang="cpp"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">parse_basic_entry</span><span class="p">();</span></span>
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4294
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4296
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<pre style="margin: 0;"> <span id="LC4296" class="line" lang="cpp"> <span class="n" style="color: #333;">POS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_POS</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4798" 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="4800" 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">@@ -4798,7 +4800,7 @@ void variant_file::output_indv_relatedness_Yang(const parameters ¶ms)</td>
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4798
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4800
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<pre style="margin: 0;"> <span id="LC4800" class="line" lang="cpp"></span>
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4799
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4801
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<pre style="margin: 0;"> <span id="LC4801" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">variant_file</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">output_PCA</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">)</span></span>
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4800
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4802
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<pre style="margin: 0;"> <span id="LC4802" class="line" lang="cpp"><span class="p">{</span></span>
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4801
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<pre style="margin: 0;">-<span id="LC4801" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left right">ndef VCFTOOLS_PCA</span></span></span>
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4803
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<pre style="margin: 0;">+<span id="LC4803" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left right"> !(HAVE_LIBLAPACK)</span></span></span>
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4802
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4804
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<pre style="margin: 0;"> <span id="LC4804" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Cannot run PCA analysis. Vcftools has been compiled without PCA enabled (requires LAPACK)."</span><span class="p">;</span></span>
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4803
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4805
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<pre style="margin: 0;"> <span id="LC4805" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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4804
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4806
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<pre style="margin: 0;"> <span id="LC4806" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4975" 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">@@ -4973,7 +4975,7 @@ void variant_file::output_PCA_SNP_loadings(const parameters ¶ms)</td>
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4973
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4975
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<pre style="margin: 0;"> <span id="LC4975" class="line" lang="cpp"><span class="p">{</span></span>
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4974
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4976
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<pre style="margin: 0;"> <span id="LC4976" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// TODO: This function duplicates a lot of what is in the output PCA function. Would be better to combine in a more</span></span>
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4975
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4977
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<pre style="margin: 0;"> <span id="LC4977" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// sensible fashion.</span></span>
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4976
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<pre style="margin: 0;">-<span id="LC4976" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left right">ndef VCFTOOLS_PCA</span></span></span>
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4978
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<pre style="margin: 0;">+<span id="LC4978" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if<span class="idiff left right"> !(HAVE_LIBLAPACK)</span></span></span>
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4977
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4979
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<pre style="margin: 0;"> <span id="LC4979" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Cannot run PCA analysis. Vcftools has been compiled without PCA enabled (requires LAPACK)."</span><span class="p">;</span></span>
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4978
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4980
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<pre style="margin: 0;"> <span id="LC4980" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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4979
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4981
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<pre style="margin: 0;"> <span id="LC4981" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" Manpage for vcftools.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.TH vcftools man page 1 "<span class="idiff left right">05 January 2016" "0.1.14</span>" "vcftools man page"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH vcftools man page 1 "<span class="idiff left right">2 August 2018" "0.1.16</span>" "vcftools man page"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">vcftools v0.1.1<span class="idiff left right">4</span> \- Utilities for the variant call format (VCF) and binary variant call format (BCF)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">vcftools v0.1.1<span class="idiff left right">6</span> \- Utilities for the variant call format (VCF) and binary variant call format (BCF)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">.B vcftools</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">[</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">@@ -772,6 +772,6 @@ This option calculates a discordance matrix. This option only works with bi-alle</td>
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="plaintext">This option calculates phasing errors (specifically "switch errors"). This option creates an output file describing switch errors found between sites, with suffix ".diff.switch".</span>
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="plaintext">.RE</span>
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="plaintext">.SH AUTHORS</span>
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="plaintext">Adam Auton<span class="idiff left right"> (adam.auton@einstein.yu.edu)</span></span>
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="plaintext">Adam Auton</span>
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="plaintext">Anthony Marcketta<span class="idiff left right"> (anthony.marcketta@einstein.yu.edu)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="plaintext">Anthony Marcketta</span></pre>
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<li id="054442b8ef7093877e9e3cdb4f96a34eb4f6918e">
<a href="https://salsa.debian.org/med-team/vcftools/commit/99c96e52d046db580495e88bde6083d63e641040#054442b8ef7093877e9e3cdb4f96a34eb4f6918e"><strong>src/perl/FaSlice.pm</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">@@ -102,7 +102,7 @@ sub cache_chr_lengths</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$line</span><span class="o" style="font-weight: 600;">=<</span><span class="nv" style="color: teal;">$fh</span><span class="o" style="font-weight: 600;">></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@items</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\t/</span><span class="p">,</span><span class="nv" style="color: teal;">$line</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$chr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$<span class="idiff left">$self</span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">chr_naming</span></span><span class="p"><span class="idiff">}</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: teal;"><span class="idiff right">$</span>items</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$chr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$items</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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106
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="perl"> <span class="nv" style="color: teal;">$$self</span><span class="p">{</span><span class="nv" style="color: teal;">chr_lengths</span><span class="p">}{</span><span class="nv" style="color: teal;">$chr</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$items</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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107
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="perl"> <span class="p">}</span></span>
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: teal;">$fh</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: teal;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">throw</span><span class="p">(</span><span class="s" style="color: #d14;">"close $$self{file}.fai"</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/vcftools/commit/99c96e52d046db580495e88bde6083d63e641040#02d15e2306b36f34d0287e5b446a7447ecaa2027"><strong>src/perl/Vcf.pm</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">@@ -2351,7 +2351,7 @@ sub validate_info_field</td>
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<pre style="margin: 0;"> <span id="LC2351" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$nr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2352
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2352
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<pre style="margin: 0;"> <span id="LC2352" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$$self</span><span class="p">{</span><span class="nv" style="color: teal;">version</span><span class="p">}</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">4.0</span> <span class="p">)</span></span>
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2353
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2353
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<pre style="margin: 0;"> <span id="LC2353" class="line" lang="perl"> <span class="p">{</span></span>
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2354
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<pre style="margin: 0;">-<span id="LC2354" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$$alts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">'.'</span> <span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$ng</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nv" style="color: teal;">$na</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2354" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$$alts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">'.'</span> <span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$ng</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nv" style="color: teal;">$na</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nv" style="color: teal;"><span class="idiff left">$nr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2355" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC2356" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2357" class="line" lang="perl"> <span class="nv" style="color: teal;">$na</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">@$alts</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/vcftools/commit/99c96e52d046db580495e88bde6083d63e641040#3d2697ef3bf18ced3cb8b5ac37ba393e1e4e8895"><strong>src/perl/vcf-haplotypes</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">@@ -24,7 +24,7 @@ sub error</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="mosel"> <span class="n" style="color: #333;">croak</span> <span class="p">@</span><span class="n" style="color: #333;">msg</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="mosel"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="mosel"> <span class="n" style="color: #333;">die</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="mosel"> <span class="s2" style="color: #d14;">"Usage: cat ref.fa | vcf-<span class="idiff left right">consensu</span>s [OPTIONS] in.vcf.gz </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"> <span class="s2" style="color: #d14;">"Usage: cat ref.fa | vcf-<span class="idiff left right">haplotype</span>s [OPTIONS] in.vcf.gz </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="mosel"> <span class="s2" style="color: #d14;">"Options:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="mosel"> <span class="s2" style="color: #d14;">" -h, -?, --help This help message.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="mosel"> <span class="s2" style="color: #d14;">" -H, --haplotypes [<int>] Apply variants for the given haplotypes (1,2). If not given, both haplotypes are applied.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">,</span></span>
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