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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/plink1-9">Debian Med / plink1.9</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/plink1-9/-/commit/e500885c208060c2b05f56b83f1624fd57887307">e500885c</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-03-25T16:17:02+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump changelog
</pre>
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<strong><a href="https://salsa.debian.org/med-team/plink1-9/-/commit/f4d078303cee5d2c1f774911622ead433c902bfe">f4d07830</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2020-03-25T16:17:58+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.90~b6.16-200219</pre>
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<strong><a href="https://salsa.debian.org/med-team/plink1-9/-/commit/67558f8c437eb1bf513f57a844ab2bbdc43b7892">67558f8c</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2020-03-25T16:18:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.90_b6.16-200219'
Update to upstream version '1.90~b6.16-200219'
with Debian dir 7bf761dba5329d4c00e14d73bd809edd21adb025</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#ce544ebebfbabf03afff4b98aa2aff1785670f6f">
debian/upstream.docs/upstream.changelog
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<li class="file-stats">
<a href="#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">
plink.c
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<li class="file-stats">
<a href="#f101da6685d6d3284ff66b606e058f55eebde6b7">
plink_data.c
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/23318f2d456b0ab6b0f4af1fc649a8e33117dca9...67558f8c437eb1bf513f57a844ab2bbdc43b7892#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">plink1.9 (1.90~b6.16-200219-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> Wed, 25 Mar 2020 16:14:14 +0100</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">plink1.9 (1.90~b6.16-200217-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream release.</span>
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<li id="ce544ebebfbabf03afff4b98aa2aff1785670f6f">
<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/23318f2d456b0ab6b0f4af1fc649a8e33117dca9...67558f8c437eb1bf513f57a844ab2bbdc43b7892#ce544ebebfbabf03afff4b98aa2aff1785670f6f"><strong>debian/upstream.docs/upstream.changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Copy/Paste from https://www.cog-genomics.org/plink/1.9/</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">1<span class="idiff left right">7</span> Feb 2020: --bcf now parses header line IDX fields; previously, if e.g. a FILTER key and an INFO key were identical in a BCFv2.2 file, --bcf may have computed the wrong string index for FORMAT:GT, in which case import would fail.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">1<span class="idiff left right">9</span> Feb 2020: --bcf now parses header line IDX fields; previously, if e.g. a FILTER key and an INFO key were identical in a BCFv2.2 file, --bcf may have computed the wrong string index for FORMAT:GT, in which case import would fail.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">21 Jan: "--extract range" and "--exclude range" no longer error out when their input files contain a chromosome code absent from the current dataset.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<li id="51f8eb620082fc9790d42dd3edff7bdbfdef0bfb">
<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/23318f2d456b0ab6b0f4af1fc649a8e33117dca9...67558f8c437eb1bf513f57a844ab2bbdc43b7892#51f8eb620082fc9790d42dd3edff7bdbfdef0bfb"><strong>plink.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -105,7 +105,7 @@ static const char ver_str[] =</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> <span class="s" style="color: #d14;">" 32-bit"</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"> <span class="s" style="color: #d14;">" (1<span class="idiff left right">7</span> Feb 2020)"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="s" style="color: #d14;">" (1<span class="idiff left right">9</span> Feb 2020)"</span><span class="p">;</span></span>
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109
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ver_str2</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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110
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// include leading space if day < 10, so character length stays the same</span></span>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="s" style="color: #d14;">""</span></span>
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<li id="f101da6685d6d3284ff66b606e058f55eebde6b7">
<a href="https://salsa.debian.org/med-team/plink1-9/-/compare/23318f2d456b0ab6b0f4af1fc649a8e33117dca9...67558f8c437eb1bf513f57a844ab2bbdc43b7892#f101da6685d6d3284ff66b606e058f55eebde6b7"><strong>plink_data.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9085" 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="9085" 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">@@ -9085,7 +9085,8 @@ int32_t bcf_header_line_idx_check(char* line_iter, char* line_end, uint32_t* gt_</td>
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9085
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9085
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<pre style="margin: 0;"> <span id="LC9085" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">','</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9086" 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">
9086
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9086
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<pre style="margin: 0;"> <span id="LC9086" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="9087" 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">
9087
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9087
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<pre style="margin: 0;"> <span id="LC9087" class="line" lang="c"> <span class="p">}</span></span>
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9088
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<pre style="margin: 0;">-<span id="LC9088" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="p">{</span></span>
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9088
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<pre style="margin: 0;">+<span id="LC9088" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// bugfix (19 Feb 2020)</span></span>
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9089
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<pre style="margin: 0;">+<span id="LC9089" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cc</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">)</span> <span class="p">{</span></span>
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9089
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9090
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<pre style="margin: 0;"> <span id="LC9090" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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9090
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9091
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<pre style="margin: 0;"> <span id="LC9091" class="line" lang="c"> <span class="p">}</span></span>
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9091
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9092
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<pre style="margin: 0;"> <span id="LC9092" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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