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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/mapdamage">Debian Med / mapdamage</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/4ae67b6e366edb1deff9061947c4a08f3e8def5d">4ae67b6e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-08T21:38:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.9+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/a80a5d97344a94550732aa4d78436e5f61370617">a80a5d97</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-08T21:38:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.0.9+dfsg'
Update to upstream version '2.0.9+dfsg'
with Debian dir b6a5d94ab06db27eb4838fb7bae3b676cb1aade7</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/d58d96055fcdbfa58789bc6115d11d98485f85d7">d58d9605</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-08T21:38:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/3c964fc6351a47a1fe574e61baf4fb079949b2a0">3c964fc6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-08T21:38:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/805f45f85de1b40c9a1621d9aae20a55d3434f71">805f45f8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-08T21:38:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/rules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/3c484663e67fa5595048daa173d0ec1e88269a11">3c484663</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-08T21:41:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#d97202d39b17c50fc83c976a09e5c652fcdb217c">
mapdamage/Rscripts/stats/function.R
</a>
</li>
<li class="file-stats">
<a href="#f1abf675c9546a833e1e6a8ab63806c189f1d0e5">
mapdamage/seq.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/8ad2d6e981d61f0a84c0889c57caf2c414d79978...3c484663e67fa5595048daa173d0ec1e88269a11#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mapdamage (2.0.9+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
</pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Remove trailing whitespace in debian/rules</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 08 Dec 2018 22:38:50 +0100</span>
</pre>
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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">mapdamage (2.0.8+dfsg-2) unstable; urgency=medium</span>
</pre>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="39" 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="47" 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">@@ -39,7 +47,7 @@ mapdamage (2.0.6+dfsg-2) unstable; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="39" 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="47" 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="LC47" class="line" lang="plaintext"> r-cran-rcppgsl package</span>
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<td class="diff-line-num old_line" data-linenumber="40" 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="48" 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="LC48" class="line" lang="plaintext"> * Edit path to seqtk in composition.py</span>
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<td class="diff-line-num old_line" data-linenumber="41" 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="49" 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="LC49" class="line" lang="plaintext"> Closes: #859090</span>
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<td class="diff-line-num old old_line" data-linenumber="42" 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="LC42" class="line" lang="plaintext"> * Fix typo in tests/control<span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="43" 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="LC50" class="line" lang="plaintext"> * Fix typo in tests/control</span>
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<td class="diff-line-num old_line" data-linenumber="43" 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="51" 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="LC51" class="line" lang="plaintext"> * Add patch to fix quantile call to remove NA and NaNs</span>
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<td class="diff-line-num old_line" data-linenumber="44" 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="52" 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="LC52" class="line" lang="plaintext"> * Add dependency providing liblapack.so and libblas.so</span>
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<td class="diff-line-num old_line" data-linenumber="45" 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="LC53" class="line" lang="plaintext"> Closes: #859091</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">@@ -47,7 +55,7 @@ mapdamage (2.0.6+dfsg-2) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> * Add information how to check R libraries and what to do in case of errors</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> to README.test</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> * Provide tests for examples from documentation</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> Closes: #848326<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> Closes: #848326</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> * Fixed typo in README.test</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> -- Nadiya Sitdykova <rovenskasa@gmail.com> Thu, 23 Mar 2017 21:34:41 -0700</span>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/8ad2d6e981d61f0a84c0889c57caf2c414d79978...3c484663e67fa5595048daa173d0ec1e88269a11#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -17,4 +17,4 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> mv `find debian -name rescale_test.py` $(TESTDIR)</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> sed -i 's/^import rescale/from mapdamage &/' $(TESTDIR)/rescale_test.py</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"><span class="idiff left right"> </span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/8ad2d6e981d61f0a84c0889c57caf2c414d79978...3c484663e67fa5595048daa173d0ec1e88269a11#d97202d39b17c50fc83c976a09e5c652fcdb217c"><strong>mapdamage/Rscripts/stats/function.R</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">@@ -145,7 +145,7 @@ seqProbVecLambda <- function(lambda,lambda_disp,m,fo_only=NA,re_only=NA){</td>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="r"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#The following is an MC simulation code to mimic the </span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#nick frequency part in the model from Philip</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="r"><span class="n" style="color: #333;">seqProbVecNuWithLengths</span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cxxfunction</span><span class="p">(</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span><span class="n" style="color: #333;">signature</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="r"><span class="n" style="color: #333;">seqProbVecNuWithLengths</span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cxxfunction</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">methods</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">signature</span><span class="p">(</span></span>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">I_la</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"numeric"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">I_la_disp</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"numeric"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">I_nu</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"numeric"</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -270,7 +270,7 @@ logLikFunOneBaseSlow <- function(Gen,S,Theta,deltad,deltas,laVec,nuVec,m,lin){</td>
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270
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="r"></span>
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271
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#The same logic as in logLikFunOneBaseSlow except using a compiled code </span></span>
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272
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#to do the hard work</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="r"><span class="n" style="color: #333;">logLikFunOneBaseFast</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cxxfunction</span><span class="p">(</span><span class="n" style="color: #333;">signature</span><span class="p">(</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="r"><span class="n" style="color: #333;">logLikFunOneBaseFast</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cxxfunction</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">methods</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">signature</span><span class="p">(</span></span>
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274
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">I_Gen</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"numeric"</span><span class="p">,</span></span>
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275
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">I_S</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"numeric"</span><span class="p">,</span></span>
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276
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">I_Theta</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"numeric"</span><span class="p">,</span></span>
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<li id="f1abf675c9546a833e1e6a8ab63806c189f1d0e5">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/8ad2d6e981d61f0a84c0889c57caf2c414d79978...3c484663e67fa5595048daa173d0ec1e88269a11#f1abf675c9546a833e1e6a8ab63806c189f1d0e5"><strong>mapdamage/seq.py</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">@@ -63,6 +63,12 @@ def read_fasta_index(filename):</td>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">print_err</span><span class="p">(</span><span class="s" style="color: #d14;">"Column 2 in FASTA index did not contain a number, found '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s':"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">ref</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">fai</span><span class="p">:</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Index for </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r does contain any sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,))</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">" Please ensure that FASTA file is valid, and</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">" re-index file using 'samtool faidx'.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fai</span></span>
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67
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<td class="diff-line-num new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="68" 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">
68
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<td class="diff-line-num 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">
74
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"></span>
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