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GitLab

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<h3>

Benjamin Redelings pushed to branch master

at <a href="https://salsa.debian.org/med-team/bali-phy">Debian Med / bali-phy</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/bali-phy/commit/beb9d2d2e0edf9f5267ee981d6cbf644bd08d132">beb9d2d2</a></strong>

<div>

<span>by Benjamin Redelings</span>

<i>at 2018-06-25T21:39:04-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bali-phy/commit/d92888bb0d8c0d4fe0c101a429bef182c6d9ca65">d92888bb</a></strong>

<div>

<span>by Benjamin Redelings</span>

<i>at 2018-06-25T21:39:07-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.2+dfsg'

Update to upstream version '3.2+dfsg'

with Debian dir 4d8bb8cc82385ed22f47beb4f2bf00a4e48754b6</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/bali-phy/commit/a40d3759c24095072e4481ced05d83543aada7c5">a40d3759</a></strong>

<div>

<span>by Benjamin Redelings</span>

<i>at 2018-06-25T21:39:49-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog.

</pre>

</li>

</ul>

<h4>18 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">

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+

NEWS

</span>

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

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<li class="file-stats">

<a href="#b89d65cbf95763f64793c7783d755624bf51e1cf">

doc/README.html

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<li class="file-stats">

<a href="#e26903080922fed937b6d35e65a8428fb2361d62">

doc/README.itex.xml

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<li class="file-stats">

<a href="#81ea4a51a393287db60c435548408876ef34189e">

doc/README.pdf

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<li class="file-stats">

<a href="#3439b2366791301eeb9f98394b5f7740fba15089">

doc/README.xhtml

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<li class="file-stats">

<a href="#e125d275f37ec5a578f0297c3809f0ee90f9172b">

examples/models/CoalMine.hs

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<li class="file-stats">

<a href="#08026a676e400b8e8ff2249986683711897d9aa1">

functions/rs07_relaxed_rates.json

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<li class="file-stats">

<a href="#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">

meson.build

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<a href="#084fd92134dca1a928080e561b8573277c2f7609">

scripts/bp-analyze

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<a href="#7737234f8646445ec91cc3054366c218c54c92d8">

src/builtins/Distribution.cc

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<a href="#b4eb2415f36da696dfb3e0536b3eca86a947ff5b">

src/builtins/SMC.cc

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<li class="file-stats">

<a href="#5658f2b4f3a4f6cfedcbe6182ff69ec8c818ff46">

src/mcmc/sample-two-nodes.cc

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<li class="file-stats">

<a href="#cee142ff88dc5968288cf8e6adf24f1cf67facdf">

src/models/rules.cc

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<a href="#94c1320ff59df5a7dbd1f999929b578c570fd365">

src/models/setup.cc

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<li class="file-stats">

<a href="#904995394c50a686a92b0e3e3164e7b530b14385">

src/tools/alignment-compare.cc

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<a href="#f309b9d7792dc999516170b579b783e20b312e55">

src/tools/alignment-identity.cc

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<li class="file-stats">

<a href="#d6a2673b0c73795d4dd427b89696a0ff5bd3c84e">

src/tools/alignment-smc.cc

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</ul>

<h4>Changes:</h4>

<li id="9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8"><strong>NEWS</strong></a>

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">* 3.2.0</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">  - Fixes</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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<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">

3

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">    - Increase test timeout for internal testsuite and testiphy.</span>

</pre>

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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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">    - HTML report: don't hide header behind top-bar in Chrome.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  - alignment-smc improvements.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">* 3.1.5</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" 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">

7

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  - Fixes</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" 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">

8

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">    - Make all programs use shipped libstdc++</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="9" 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">

9

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">    - Make MDS plots handle bp-analyze --subsample</span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">    - Increase test timeouts</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="11" 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">

11

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">    - Correctly write initial alignment for fixed alignment partitions.</span>

</pre>

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12

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">    - Don't write "file:" for MDS URLs in HTML report</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="13" 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">

13

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">  - Print citations with pmid and pmcid in help.</span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">  - Add Frequencies.uniform[] function.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="15" 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">

15

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">  - Print help for 0-argument functions like 'dna'</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16" 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">

16

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">  - Make SEV handle site-compression.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" 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">

17

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">  - HTML report: print version number + lots of cosmetic improvements.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" 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">

18

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">  - Add new tool tree-tool (and map page, etc.)</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" 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">

19

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">  - Change alignments-diff highlight color back to red.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" 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">

20

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">  - Clean up DP matrix code.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="21" 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">

21

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">* 3.1.4</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" 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">

22

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">  - Fix prior on alpha in Rates.gamma</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" 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">

23

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">* 3.1.3</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" 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">

24

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">  - Fix mean_length prior in RS05 model.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">  - Add some more color-schemes for drawing alignments-diff output.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" 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">

26

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">  - Add ferns exon/intro data set.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" 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">

27

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">* 3.1.2</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" 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">

28

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">  - Fix a testsuite bug</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="29" 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">

29

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">* 3.1.1</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" 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">

30

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">  - Print priors on models in their own section.</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder new" id="" style="line-height: 1.6;">

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</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bali-phy (3.2+dfsg-1) UNRELEASED; urgency=medium</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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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<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">

3

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="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">

4

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Benjamin Redelings <benjamin.redelings@gmail.com>  Mon, 25 Jun 2018 21:39:12 -0400</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

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1

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<td class="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext">bali-phy (3.1.5+dfsg-1) unstable; urgency=medium</span>

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2

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<td class="diff-line-num new_line" data-linenumber="8" 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">

8

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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 version</span>

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<li id="b89d65cbf95763f64793c7783d755624bf51e1cf">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#b89d65cbf95763f64793c7783d755624bf51e1cf"><strong>doc/README.html</strong></a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="html"><span class="nt" style="color: navy;"><html><head><meta</span> <span class="na" style="color: teal;">http-equiv=</span><span class="s" style="color: #d14;">"Content-Type"</span> <span class="na" style="color: teal;">content=</span><span class="s" style="color: #d14;">"text/html; charset=ISO-8859-1"</span><span class="nt" style="color: navy;">><title></span>BAli-Phy User's Guide v3.<span class="idiff left">1</span><span class="nt" style="color: navy;"><span class="idiff"></title><link</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">rel=</span></span><span class="s" style="color: #d14;"><span class="idiff">"stylesheet"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">type=</span></span><span class="s" style="color: #d14;"><span class="idiff">"text/css"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docbook.css"</span></span><span class="nt" style="color: navy;"><span class="idiff">><meta</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">"generator"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">content=</span></span><span class="s" style="color: #d14;"><span class="idiff">"DocBook XSL Stylesheets V1.79.1"</span></span><span class="nt" style="color: navy;"><span class="idiff">></head><body</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">bgcolor=</span></span><span class="s" style="color: #d14;"><span class="idiff">"white"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">text=</span></span><span class="s" style="color: #d14;"><span class="idiff">"black"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">link=</span></span><span class="s" style="color: #d14;"><span class="idiff">"#0000FF"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">vlink=</span></span><span class="s" style="color: #d14;"><span class="idiff">"#840084"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">alink=</span></span><span class="s" style="color: #d14;"><span class="idiff">"#0000FF"</span></span><span class="nt" style="color: navy;"><span class="idiff">><div</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">lang=</span></span><span class="s" style="color: #d14;"><span class="idiff">"en"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"article"</span></span><span class="nt" style="color: navy;"><span class="idiff">><div</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"titlepage"</span></span><span class="nt" style="color: navy;"><span class="idiff">><div><div><h2</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"title"</span></span><span class="nt" style="color: navy;"><span class="idiff">><a</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">"idp1"</span></span><span class="nt" style="color: navy;"><span class="idiff">></a><span</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"application"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">BAli-Phy</span><span class="nt" style="color: navy;"><span class="idiff"></span></span></span><span class="idiff right"> User's Guide v3.1</span><span class="nt" style="color: navy;"></h2></div><div><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"author"</span><span class="nt" style="color: navy;">><h3</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"author"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"firstname"</span><span class="nt" style="color: navy;">></span>Benjamin<span class="nt" style="color: navy;"></span></span> <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"surname"</span><span class="nt" style="color: navy;">></span>Redelings<span class="nt" style="color: navy;"></span></h3></div></div></div><hr></div><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"toc"</span><span class="nt" style="color: navy;">><p><b></span>Table of Contents<span class="nt" style="color: navy;"></b></p><dl</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"toc"</span><span class="nt" style="color: navy;">><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#intro"</span><span class="nt" style="color: navy;">></span>1. Introduction<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#installation"</span><span class="nt" style="color: navy;">></span>2. Installation<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#pre-requisites"</span><span class="nt" style="color: navy;">></span>2.1. Hardware requirements<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp5"</span><span class="nt" style="color: navy;">></span>2.2. Install on MS Windows<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp10"</span><span class="nt" style="color: navy;">></span>2.3. Install on Mac OS X<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp15"</span><span class="nt" style="color: navy;">></span>2.4. Install on Linux<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#path"</span><span class="nt" style="color: navy;">></span>2.5. Add BAli-Phy to your <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"envar"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></code></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#tests"</span><span class="nt" style="color: navy;">></span>2.6. Test the installed software<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#software_req"</span><span class="nt" style="color: navy;">></span>2.7. Install programs used for viewing the results<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#compilation"</span><span class="nt" style="color: navy;">></span>3. Compiling <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"application"</span><span class="nt" style="color: navy;">></span>BAli-Phy<span class="nt" style="color: navy;"></span></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp25"</span><span class="nt" style="color: navy;">></span>3.1. Setup<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#quickstart"</span><span class="nt" style="color: navy;">></span>3.2. Clone, Configure, Compile<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp26"</span><span class="nt" style="color: navy;">></span>3.3. Options: compiler and linker flags<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#running"</span><span class="nt" style="color: navy;">></span>4. Running the program<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp27"</span><span class="nt" style="color: navy;">></span>4.1. Quick Start<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp28"</span><span class="nt" style="color: navy;">></span>4.2. Command line options<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp33"</span><span class="nt" style="color: navy;">></span>4.3. Multiple genes/partitions, models, and linking<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#cluster"</span><span class="nt" style="color: navy;">></span>4.4. Running on computing clusters<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp37"</span><span class="nt" style="color: navy;">></span>4.5. Option files (Scripts)<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#examples"</span><span class="nt" style="color: navy;">></span>4.6. Examples<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#input"</span><span class="nt" style="color: navy;">></span>5. Input<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp38"</span><span class="nt" style="color: navy;">></span>5.1. Sequence formats<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp41"</span><span class="nt" style="color: navy;">></span>5.2. Is my data set too large?<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#output"</span><span class="nt" style="color: navy;">></span>6. Output<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp42"</span><span class="nt" style="color: navy;">></span>6.1. Output directory<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp46"</span><span class="nt" style="color: navy;">></span>6.2. Output files<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp54"</span><span class="nt" style="color: navy;">></span>6.3. Summarizing the output<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#analysis"</span><span class="nt" style="color: navy;">></span>6.4. Summarizing the output - scripted<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#functions"</span><span class="nt" style="color: navy;">></span>7. Models and Priors<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp57"</span><span class="nt" style="color: navy;">></span>7.1. Models and distributions are functions<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#priors"</span><span class="nt" style="color: navy;">></span>7.2. Priors<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp61"</span><span class="nt" style="color: navy;">></span>7.3. Models and '<span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>+<span class="nt" style="color: navy;"></code></strong></span>' notation<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#default_values"</span><span class="nt" style="color: navy;">></span>7.4. Default values and default priors<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#types"</span><span class="nt" style="color: navy;">></span>7.5. Argument and result types<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#subst_models"</span><span class="nt" style="color: navy;">></span>8. Substitution models<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp62"</span><span class="nt" style="color: navy;">></span>8.1. Default substitution models<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#subst_basic"</span><span class="nt" style="color: navy;">></span>8.2. Basic CTMC models<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#subst_freq"</span><span class="nt" style="color: navy;">></span>8.3. Substitution Frequency models<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp63"</span><span class="nt" style="color: navy;">></span>8.4. Substitution Mixture Models<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp64"</span><span class="nt" style="color: navy;">></span>8.5. The branch-site substitution model<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp65"</span><span class="nt" style="color: navy;">></span>8.6. Substitution model examples<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#genetic-codes"</span><span class="nt" style="color: navy;">></span>8.7. Genetic Codes<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#indel_models"</span><span class="nt" style="color: navy;">></span>9. Insertion/deletion models<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#mixing_and_convergence"</span><span class="nt" style="color: navy;">></span>10. Convergence and Mixing: Is it done yet?<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp66"</span><span class="nt" style="color: navy;">></span>10.1. Definition of Convergence<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp67"</span><span class="nt" style="color: navy;">></span>10.2. Definition of Mixing<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp70"</span><span class="nt" style="color: navy;">></span>10.3. Diagnostics: Variation in split frequencies across runs (ASDSF/MSDSF)<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp71"</span><span class="nt" style="color: navy;">></span>10.4. Diagnostics: Potential Scale Reduction Factors (PSRF)<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp74"</span><span class="nt" style="color: navy;">></span>10.5. Diagnostics: Effective sample sizes (ESS)<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp77"</span><span class="nt" style="color: navy;">></span>10.6. Diagnostics: Stabilization<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#alignment-utilities"</span><span class="nt" style="color: navy;">></span>11. Alignment utilities<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp78"</span><span class="nt" style="color: navy;">></span>11.1. alignment-info<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp79"</span><span class="nt" style="color: navy;">></span>11.2. alignment-cat<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp80"</span><span class="nt" style="color: navy;">></span>11.3. alignment-thin<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp81"</span><span class="nt" style="color: navy;">></span>11.4. alignment-draw<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp82"</span><span class="nt" style="color: navy;">></span>11.5. alignment-find<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp83"</span><span class="nt" style="color: navy;">></span>11.6. alignment-indices<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp84"</span><span class="nt" style="color: navy;">></span>11.7. alignment-chop-internal<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#tree-utilities"</span><span class="nt" style="color: navy;">></span>12. Tree utilities<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp85"</span><span class="nt" style="color: navy;">></span>12.1. trees-consensus<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp86"</span><span class="nt" style="color: navy;">></span>12.2. trees-bootstrap<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp87"</span><span class="nt" style="color: navy;">></span>12.3. trees-to-SRQ<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#FAQ"</span><span class="nt" style="color: navy;">></span>13. Frequently Asked Questions (FAQ)<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp88"</span><span class="nt" style="color: navy;">></span>13.1. Input files<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp89"</span><span class="nt" style="color: navy;">></span>13.2. Running <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bali-phy<span class="nt" style="color: navy;"></strong></span></span>.<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp90"</span><span class="nt" style="color: navy;">></span>13.3. Run-time error messages<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp91"</span><span class="nt" style="color: navy;">></span>13.4. Stopping <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bali-phy<span class="nt" style="color: navy;"></strong></span></span>.<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp92"</span><span class="nt" style="color: navy;">></span>13.5. Running <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bp-analyze<span class="nt" style="color: navy;"></strong></span></span>.<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp93"</span><span class="nt" style="color: navy;">></span>13.6. Interpreting the results.<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp94"</span><span class="nt" style="color: navy;">></span>13.7. How do I...<span class="nt" style="color: navy;"></a></span></dt></dl></dd></dl></div></span></span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="html"><span class="nt" style="color: navy;"><html><head><meta</span> <span class="na" style="color: teal;">http-equiv=</span><span class="s" style="color: #d14;">"Content-Type"</span> <span class="na" style="color: teal;">content=</span><span class="s" style="color: #d14;">"text/html; charset=ISO-8859-1"</span><span class="nt" style="color: navy;">><title></span>BAli-Phy User's Guide v3.<span class="idiff left">2</span><span class="nt" style="color: navy;"><span class="idiff"></title><link</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">rel=</span></span><span class="s" style="color: #d14;"><span class="idiff">"stylesheet"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">type=</span></span><span class="s" style="color: #d14;"><span class="idiff">"text/css"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"docbook.css"</span></span><span class="nt" style="color: navy;"><span class="idiff">><meta</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">"generator"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">content=</span></span><span class="s" style="color: #d14;"><span class="idiff">"DocBook XSL Stylesheets V1.79.1"</span></span><span class="nt" style="color: navy;"><span class="idiff">></head><body</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">bgcolor=</span></span><span class="s" style="color: #d14;"><span class="idiff">"white"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">text=</span></span><span class="s" style="color: #d14;"><span class="idiff">"black"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">link=</span></span><span class="s" style="color: #d14;"><span class="idiff">"#0000FF"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">vlink=</span></span><span class="s" style="color: #d14;"><span class="idiff">"#840084"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">alink=</span></span><span class="s" style="color: #d14;"><span class="idiff">"#0000FF"</span></span><span class="nt" style="color: navy;"><span class="idiff">><div</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">lang=</span></span><span class="s" style="color: #d14;"><span class="idiff">"en"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"article"</span></span><span class="nt" style="color: navy;"><span class="idiff">><div</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"titlepage"</span></span><span class="nt" style="color: navy;"><span class="idiff">><div><div><h2</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"title"</span></span><span class="nt" style="color: navy;"><span class="idiff">><a</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">name=</span></span><span class="s" style="color: #d14;"><span class="idiff">"idp1"</span></span><span class="nt" style="color: navy;"><span class="idiff">></a><span</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"application"</span></span><span class="nt" style="color: navy;"><span class="idiff">></span></span><span class="idiff">BAli-Phy</span><span class="nt" style="color: navy;"><span class="idiff"></span></span></span><span class="idiff right"> User's Guide v3.2</span><span class="nt" style="color: navy;"></h2></div><div><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"author"</span><span class="nt" style="color: navy;">><h3</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"author"</span><span class="nt" style="color: navy;">><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"firstname"</span><span class="nt" style="color: navy;">></span>Benjamin<span class="nt" style="color: navy;"></span></span> <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"surname"</span><span class="nt" style="color: navy;">></span>Redelings<span class="nt" style="color: navy;"></span></h3></div></div></div><hr></div><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"toc"</span><span class="nt" style="color: navy;">><p><b></span>Table of Contents<span class="nt" style="color: navy;"></b></p><dl</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"toc"</span><span class="nt" style="color: navy;">><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#intro"</span><span class="nt" style="color: navy;">></span>1. Introduction<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#installation"</span><span class="nt" style="color: navy;">></span>2. Installation<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#pre-requisites"</span><span class="nt" style="color: navy;">></span>2.1. Hardware requirements<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp5"</span><span class="nt" style="color: navy;">></span>2.2. Install on MS Windows<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp10"</span><span class="nt" style="color: navy;">></span>2.3. Install on Mac OS X<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp15"</span><span class="nt" style="color: navy;">></span>2.4. Install on Linux<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#path"</span><span class="nt" style="color: navy;">></span>2.5. Add BAli-Phy to your <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"envar"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></code></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#tests"</span><span class="nt" style="color: navy;">></span>2.6. Test the installed software<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#software_req"</span><span class="nt" style="color: navy;">></span>2.7. Install programs used for viewing the results<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#compilation"</span><span class="nt" style="color: navy;">></span>3. Compiling <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"application"</span><span class="nt" style="color: navy;">></span>BAli-Phy<span class="nt" style="color: navy;"></span></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp25"</span><span class="nt" style="color: navy;">></span>3.1. Setup<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#quickstart"</span><span class="nt" style="color: navy;">></span>3.2. Clone, Configure, Compile<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp26"</span><span class="nt" style="color: navy;">></span>3.3. Options: compiler and linker flags<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#running"</span><span class="nt" style="color: navy;">></span>4. Running the program<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp27"</span><span class="nt" style="color: navy;">></span>4.1. Quick Start<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp28"</span><span class="nt" style="color: navy;">></span>4.2. Command line options<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp33"</span><span class="nt" style="color: navy;">></span>4.3. Multiple genes/partitions, models, and linking<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#cluster"</span><span class="nt" style="color: navy;">></span>4.4. Running on computing clusters<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp37"</span><span class="nt" style="color: navy;">></span>4.5. Option files (Scripts)<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#examples"</span><span class="nt" style="color: navy;">></span>4.6. Examples<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#input"</span><span class="nt" style="color: navy;">></span>5. Input<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp38"</span><span class="nt" style="color: navy;">></span>5.1. Sequence formats<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp41"</span><span class="nt" style="color: navy;">></span>5.2. Is my data set too large?<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#output"</span><span class="nt" style="color: navy;">></span>6. Output<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp42"</span><span class="nt" style="color: navy;">></span>6.1. Output directory<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp46"</span><span class="nt" style="color: navy;">></span>6.2. Output files<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp54"</span><span class="nt" style="color: navy;">></span>6.3. Summarizing the output<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#analysis"</span><span class="nt" style="color: navy;">></span>6.4. Summarizing the output - scripted<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#functions"</span><span class="nt" style="color: navy;">></span>7. Models and Priors<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp57"</span><span class="nt" style="color: navy;">></span>7.1. Models and distributions are functions<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#priors"</span><span class="nt" style="color: navy;">></span>7.2. Priors<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp61"</span><span class="nt" style="color: navy;">></span>7.3. Models and '<span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>+<span class="nt" style="color: navy;"></code></strong></span>' notation<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#default_values"</span><span class="nt" style="color: navy;">></span>7.4. Default values and default priors<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#types"</span><span class="nt" style="color: navy;">></span>7.5. Argument and result types<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#subst_models"</span><span class="nt" style="color: navy;">></span>8. Substitution models<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp62"</span><span class="nt" style="color: navy;">></span>8.1. Default substitution models<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#subst_basic"</span><span class="nt" style="color: navy;">></span>8.2. Basic CTMC models<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#subst_freq"</span><span class="nt" style="color: navy;">></span>8.3. Substitution Frequency models<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp63"</span><span class="nt" style="color: navy;">></span>8.4. Substitution Mixture Models<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp64"</span><span class="nt" style="color: navy;">></span>8.5. The branch-site substitution model<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp65"</span><span class="nt" style="color: navy;">></span>8.6. Substitution model examples<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#genetic-codes"</span><span class="nt" style="color: navy;">></span>8.7. Genetic Codes<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#indel_models"</span><span class="nt" style="color: navy;">></span>9. Insertion/deletion models<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#mixing_and_convergence"</span><span class="nt" style="color: navy;">></span>10. Convergence and Mixing: Is it done yet?<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp66"</span><span class="nt" style="color: navy;">></span>10.1. Definition of Convergence<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp67"</span><span class="nt" style="color: navy;">></span>10.2. Definition of Mixing<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp70"</span><span class="nt" style="color: navy;">></span>10.3. Diagnostics: Variation in split frequencies across runs (ASDSF/MSDSF)<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp71"</span><span class="nt" style="color: navy;">></span>10.4. Diagnostics: Potential Scale Reduction Factors (PSRF)<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp74"</span><span class="nt" style="color: navy;">></span>10.5. Diagnostics: Effective sample sizes (ESS)<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp77"</span><span class="nt" style="color: navy;">></span>10.6. Diagnostics: Stabilization<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#alignment-utilities"</span><span class="nt" style="color: navy;">></span>11. Alignment utilities<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp78"</span><span class="nt" style="color: navy;">></span>11.1. alignment-info<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp79"</span><span class="nt" style="color: navy;">></span>11.2. alignment-cat<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp80"</span><span class="nt" style="color: navy;">></span>11.3. alignment-thin<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp81"</span><span class="nt" style="color: navy;">></span>11.4. alignment-draw<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp82"</span><span class="nt" style="color: navy;">></span>11.5. alignment-find<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp83"</span><span class="nt" style="color: navy;">></span>11.6. alignment-indices<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp84"</span><span class="nt" style="color: navy;">></span>11.7. alignment-chop-internal<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#tree-utilities"</span><span class="nt" style="color: navy;">></span>12. Tree utilities<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp85"</span><span class="nt" style="color: navy;">></span>12.1. trees-consensus<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp86"</span><span class="nt" style="color: navy;">></span>12.2. trees-bootstrap<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp87"</span><span class="nt" style="color: navy;">></span>12.3. trees-to-SRQ<span class="nt" style="color: navy;"></a></span></dt></dl></dd><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#FAQ"</span><span class="nt" style="color: navy;">></span>13. Frequently Asked Questions (FAQ)<span class="nt" style="color: navy;"></a></span></dt><dd><dl><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp88"</span><span class="nt" style="color: navy;">></span>13.1. Input files<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp89"</span><span class="nt" style="color: navy;">></span>13.2. Running <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bali-phy<span class="nt" style="color: navy;"></strong></span></span>.<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp90"</span><span class="nt" style="color: navy;">></span>13.3. Run-time error messages<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp91"</span><span class="nt" style="color: navy;">></span>13.4. Stopping <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bali-phy<span class="nt" style="color: navy;"></strong></span></span>.<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp92"</span><span class="nt" style="color: navy;">></span>13.5. Running <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bp-analyze<span class="nt" style="color: navy;"></strong></span></span>.<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp93"</span><span class="nt" style="color: navy;">></span>13.6. Interpreting the results.<span class="nt" style="color: navy;"></a></span></dt><dt><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#idp94"</span><span class="nt" style="color: navy;">></span>13.7. How do I...<span class="nt" style="color: navy;"></a></span></dt></dl></dd></dl></div></span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="html">  <span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"titlepage"</span><span class="nt" style="color: navy;">><div><div><h2</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"title"</span> <span class="na" style="color: teal;">style=</span><span class="s" style="color: #d14;">"clear: both"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"intro"</span><span class="nt" style="color: navy;">></a></span>1. Introduction<span class="nt" style="color: navy;"></h2></div></div></div></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">@@ -53,10 +53,10 @@</td>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="html">  First, download and extract the executables:</span>

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<td class="diff-line-num old_line" data-linenumber="54" 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="LC54" class="line" lang="html">      <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>mkdir -p ~/Applications<span class="nt" style="color: navy;"></code></strong></span></span>

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<td class="diff-line-num new_line" data-linenumber="55" 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="LC55" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>cd ~/Applications<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>wget http://www.bali-phy.org/files/bali-phy-3.<span class="idiff left right">1</span>-win64.tar.gz<span class="nt" style="color: navy;"></code></strong></span></span>

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<td class="diff-line-num old old_line" data-linenumber="57" 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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<td class="diff-line-num new_line old" data-linenumber="56" 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="LC57" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>tar -zxf bali-phy-3.<span class="idiff left right">1</span>-win64.tar.gz<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<td class="diff-line-num new old_line" data-linenumber="58" 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="LC56" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>wget http://www.bali-phy.org/files/bali-phy-3.<span class="idiff left right">2</span>-win64.tar.gz<span class="nt" style="color: navy;"></code></strong></span></span>

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<td class="diff-line-num new old_line" data-linenumber="58" 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="LC57" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>tar -zxf bali-phy-3.<span class="idiff left right">2</span>-win64.tar.gz<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="html">       Second, check that the <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bali-phy<span class="nt" style="color: navy;"></strong></span></span> executable runs:</span>

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<td class="diff-line-num old old_line" data-linenumber="59" 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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<td class="diff-line-num new_line old" data-linenumber="59" 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="LC59" class="line" lang="html">      <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>~/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin/bali-phy --version<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="html">      <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>~/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin/bali-phy --version<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="html">      You still need to add it to your PATH as described in <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"xref"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#path"</span> <span class="na" style="color: teal;">title=</span><span class="s" style="color: #d14;">"2.5. Add BAli-Phy to your PATH"</span><span class="nt" style="color: navy;">></span>Section 2.5, <span class="ni" style="color: purple;">&#8220;</span>Add BAli-Phy to your <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"envar"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></code></span><span class="ni" style="color: purple;">&#8221;</span><span class="nt" style="color: navy;"></a></span>.</span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="html">    <span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="html"><span class="nt" style="color: navy;"></div></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" 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="81" 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">@@ -81,10 +81,10 @@ If you install with homebrew, you don't need to do anything extra to put bali-ph</td>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="html">      First download and extract the executables:</span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="html">      <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>mkdir -p ~/Applications<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>cd ~/Applications<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>curl -O http://www.bali-phy.org/files/bali-phy-3.<span class="idiff left right">1</span>-mac64.tar.gz<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>tar -zxf bali-phy-3.<span class="idiff left right">1</span>-mac64.tar.gz<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>curl -O http://www.bali-phy.org/files/bali-phy-3.<span class="idiff left right">2</span>-mac64.tar.gz<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>tar -zxf bali-phy-3.<span class="idiff left right">2</span>-mac64.tar.gz<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="html">      Check that the executable runs:</span>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="html">      <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>~/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin/bali-phy --version<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="html">      <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>~/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin/bali-phy --version<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="html">      You still need to add it to your PATH as described in <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"xref"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#path"</span> <span class="na" style="color: teal;">title=</span><span class="s" style="color: #d14;">"2.5. Add BAli-Phy to your PATH"</span><span class="nt" style="color: navy;">></span>Section 2.5, <span class="ni" style="color: purple;">&#8220;</span>Add BAli-Phy to your <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"envar"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></code></span><span class="ni" style="color: purple;">&#8221;</span><span class="nt" style="color: navy;"></a></span>.</span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="html">    <span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="html"></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">@@ -114,7 +114,8 @@ However, note that this might conflict with R installed from other places, such </td>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="html">    <span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"titlepage"</span><span class="nt" style="color: navy;">><div><div><h3</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"idp15"</span><span class="nt" style="color: navy;">></a></span>2.4. Install on Linux<span class="nt" style="color: navy;"></h3></div></div></div></span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="html"></span>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="html">    <span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"titlepage"</span><span class="nt" style="color: navy;">><div><div><h4</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"idp11"</span><span class="nt" style="color: navy;">></a></span>2.4.1. Install BAli-Phy using <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>apt-get<span class="nt" style="color: navy;"></strong></span></span> (recommended if using <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"emphasis"</span><span class="nt" style="color: navy;">><em></span>Debian: testing or unstable<span class="nt" style="color: navy;"></em></span></span>)<span class="nt" style="color: navy;"></h4></div></div></div></span></span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="html">    <span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"titlepage"</span><span class="nt" style="color: navy;">><div><div><h4</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"idp11"</span><span class="nt" style="color: navy;">></a></span>2.4.1. Install BAli-Phy using <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>apt-get<span class="nt" style="color: navy;"></strong></span></h4></div></div></div></span></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="html">    BAli-Phy is available on Ubuntu <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"ulink"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://launchpad.net/ubuntu/+source/bali-phy/"</span> <span class="na" style="color: teal;">target=</span><span class="s" style="color: #d14;">"_top"</span><span class="nt" style="color: navy;">></span>("Cosmic Cuttlefish" or later)<span class="nt" style="color: navy;"></a></span>, and Debian (<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"ulink"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://packages.debian.org/search?keywords=bali-phy&amp;searchon=names&amp;section=all"</span> <span class="na" style="color: teal;">target=</span><span class="s" style="color: #d14;">"_top"</span><span class="nt" style="color: navy;">></span>testing and unstable<span class="nt" style="color: navy;"></a></span>).</span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="html">    <span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>sudo apt-get install bali-phy<span class="nt" style="color: navy;"></code></strong></pre></span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="html">    Check that the executable runs:</span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="html">    <span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy --version<span class="nt" style="color: navy;"></code></strong></pre></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">@@ -130,10 +131,10 @@ However, note that this might conflict with R installed from other places, such </td>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="html">      Then download and extract the executables:</span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="html">      <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>mkdir -p ~/Applications<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>cd ~/Applications<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>wget http://www.bali-phy.org/files/bali-phy-3.<span class="idiff left right">1</span>-linux64.tar.gz<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>tar -zxf bali-phy-3.<span class="idiff left right">1</span>-linux64.tar.gz<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>wget http://www.bali-phy.org/files/bali-phy-3.<span class="idiff left right">2</span>-linux64.tar.gz<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>tar -zxf bali-phy-3.<span class="idiff left right">2</span>-linux64.tar.gz<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="html">      Second, check that the executable runs:</span>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="html">      <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>~/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin/bali-phy --version<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="html">      <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>~/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin/bali-phy --version<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="html">      You still need to add it to your PATH as described in <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"xref"</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#path"</span> <span class="na" style="color: teal;">title=</span><span class="s" style="color: #d14;">"2.5. Add BAli-Phy to your PATH"</span><span class="nt" style="color: navy;">></span>Section 2.5, <span class="ni" style="color: purple;">&#8220;</span>Add BAli-Phy to your <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"envar"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></code></span><span class="ni" style="color: purple;">&#8221;</span><span class="nt" style="color: navy;"></a></span>.</span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="html">    <span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="html">    <span class="nt" style="color: navy;"></div></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">@@ -166,10 +167,10 @@ If bali-phy is not in your PATH, then continue with this section.</td>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="html">    <span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="html">    <span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"titlepage"</span><span class="nt" style="color: navy;">><div><div><h4</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"idp17"</span><span class="nt" style="color: navy;">></a></span>2.5.2. Quick version<span class="nt" style="color: navy;"></h4></div></div></div></span></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Add <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bali-phy<span class="nt" style="color: navy;"></strong></span></span> to your PATH, so that the shell knows where to find it.  This command only affects the terminal in which it is typed, and will not affect new terminals:</span>

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="html"><span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>export PATH=~/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin:$PATH<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="html"><span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>export PATH=~/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin:$PATH<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="html">To set the PATH automatically for new terminals, type:</span>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="html"><span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>test -r ~/.bash_profile <span class="ni" style="color: purple;">&amp;&amp;</span> echo 'export PATH=~/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin:$PATH' <span class="ni" style="color: purple;">&gt;&gt;</span> ~/.bash_profile<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>echo 'export PATH=~/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin:$PATH' <span class="ni" style="color: purple;">&gt;&gt;</span> ~/.profile<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<td class="diff-line-num new new_line" data-linenumber="172" 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="LC172" class="line" lang="html"><span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>test -r ~/.bash_profile <span class="ni" style="color: purple;">&amp;&amp;</span> echo 'export PATH=~/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin:$PATH' <span class="ni" style="color: purple;">&gt;&gt;</span> ~/.bash_profile<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>echo 'export PATH=~/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin:$PATH' <span class="ni" style="color: purple;">&gt;&gt;</span> ~/.profile<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="html">This will affect new terminals only after you log out and log back in though.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="html"><span class="nt" style="color: navy;"><p></span></span>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="html">Now check that the executable runs:</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="182" 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="183" 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">@@ -182,7 +183,7 @@ If it does, then your PATH is set up correctly, and you can probably skip the re</td>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="html">      <span class="nt" style="color: navy;"><p></span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="html"> If you installed <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"application"</span><span class="nt" style="color: navy;">></span>BAli-Phy<span class="nt" style="color: navy;"></span></span> to the directory</span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="html"> <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>~/Applications<span class="nt" style="color: navy;"></code></span>, then you can run</span>

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<td class="diff-line-num new_line old" data-linenumber="186" 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="LC185" class="line" lang="html"> bali-phy by typing <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>~/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin/bali-phy<span class="nt" style="color: navy;"></strong></span></span>.</span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="html"> bali-phy by typing <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>~/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin/bali-phy<span class="nt" style="color: navy;"></strong></span></span>.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="html"> However, it would be much nicer to simply type</span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="html"> <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bali-phy<span class="nt" style="color: navy;"></strong></span></span> and let the computer find the</span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="html"> executable for you.  This can be achieved by putting the directory</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="206" 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">@@ -205,9 +206,9 @@ If it does, then your PATH is set up correctly, and you can probably skip the re</td>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="html"> <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>echo $PATH<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<td class="diff-line-num new_line" data-linenumber="207" 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="LC207" class="line" lang="html"> We will assume that you extracted the bali-phy archive in</span>

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<td class="diff-line-num old_line" data-linenumber="207" 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="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">

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="html"> <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>~/Applications<span class="nt" style="color: navy;"></code></span> and so you want to add</span>

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<td class="diff-line-num old old_line" data-linenumber="208" 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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<td class="diff-line-num new_line old" data-linenumber="209" 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="LC208" class="line" lang="html"> <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>$HOME/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin<span class="nt" style="color: navy;"></code></span></span>

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<td class="diff-line-num new new_line" data-linenumber="209" 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="LC209" class="line" lang="html"> <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>$HOME/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin<span class="nt" style="color: navy;"></code></span></span>

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<td class="diff-line-num new_line" data-linenumber="210" 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="LC210" class="line" lang="html"> to your <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"envar"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></code></span>.  (If you installed to another directory,</span>

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<td class="diff-line-num old old_line" data-linenumber="210" 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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<td class="diff-line-num new_line old" data-linenumber="211" 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="LC210" class="line" lang="html"> replace <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>$HOME/Applications/bali-phy-3.<span class="idiff left right">1</span>/<span class="nt" style="color: navy;"></code></span> with that directory.)</span>

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<td class="diff-line-num new old_line" data-linenumber="211" 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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<td class="diff-line-num new new_line" data-linenumber="211" 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="LC211" class="line" lang="html"> replace <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>$HOME/Applications/bali-phy-3.<span class="idiff left right">2</span>/<span class="nt" style="color: navy;"></code></span> with that directory.)</span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="html">      <span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="html">      <span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="html"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="217" 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="218" 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">@@ -217,10 +218,10 @@ If it does, then your PATH is set up correctly, and you can probably skip the re</td>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="html"> <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>echo $SHELL<span class="nt" style="color: navy;"></strong></span></span> to find out. If your</span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="html"> shell is <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>sh<span class="nt" style="color: navy;"></strong></span></span> or </span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="html"> <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bash<span class="nt" style="color: navy;"></strong></span></span> then the command looks like this: </span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="html"> <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>PATH=$HOME/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin:$PATH<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="html"> <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>PATH=$HOME/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin:$PATH<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="html"> If your shell is <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>csh<span class="nt" style="color: navy;"></strong></span></span> or</span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="html"> <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>tcsh<span class="nt" style="color: navy;"></strong></span></span>, then the command looks like this:</span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="html"> <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>setenv PATH $HOME/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin:$PATH<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="html"> <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>setenv PATH $HOME/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin:$PATH<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="html"> Note that these commands will only affect the window you are typing</span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="html"> in, and will vanish when you reboot.   </span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="html">      <span class="nt" style="color: navy;"></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">@@ -251,8 +252,8 @@ If it does, then your PATH is set up correctly, and you can probably skip the re</td>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="html">    <span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"titlepage"</span><span class="nt" style="color: navy;">><div><div><h3</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"tests"</span><span class="nt" style="color: navy;">></a></span>2.6. Test the installed software<span class="nt" style="color: navy;"></h3></div></div></div></span></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="html">    <span class="nt" style="color: navy;"><p></span>In order to determine that the software has been correctly installed, and the <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"envar"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></code></span> has been correctly set, run the following commands:</span>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="html">    <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy ~/Applications/bali-phy-3.<span class="idiff left right">1</span>/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta --iter=150<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy ~/Applications/bali-phy-3.<span class="idiff left right">1</span>/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta --iter=150<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="html">    <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy ~/Applications/bali-phy-3.<span class="idiff left right">2</span>/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta --iter=150<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy ~/Applications/bali-phy-3.<span class="idiff left right">2</span>/share/doc/bali-phy/examples/sequences/5S-rRNA/25.fasta --iter=150<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bp-analyze 25-1 25-2<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="html">    <span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="html">    <span class="nt" style="color: navy;"><p></span>Furthermore, the directories <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>25-1<span class="nt" style="color: navy;"></code></span> and <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>25-2<span class="nt" style="color: navy;"></code></span> should contain a file called <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>C1.log<span class="nt" style="color: navy;"></code></span>.  You should be able to load these files in Tracer, although the chain will not really have converged yet.<span class="nt" style="color: navy;"></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">@@ -360,9 +361,9 @@ Otherwise you can install meson through pip3:</td>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="html"><span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="html"><span class="nt" style="color: navy;"><p></span></span>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="html">Then run meson to configure the build process:</span>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="html"><span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span> meson build --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">1</span>/<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="html"><span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span> meson build --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">2</span>/<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="html">In the MSYS2 environment, the command is called <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>meson.py<span class="nt" style="color: navy;"></strong></span></span> instead of <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>meson<span class="nt" style="color: navy;"></strong></span></span>:</span>

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="html"><span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span> meson.py build --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">1</span>/<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="html"><span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span> meson.py build --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">2</span>/<span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="html"><span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="html">Finally, build and install the software:</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">@@ -370,21 +371,21 @@ Finally, build and install the software:</td>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span> ninja -C build test<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="html"><span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span> ninja -C build install<span class="nt" style="color: navy;"></code></strong></span></span>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="html"><span class="nt" style="color: navy;"></pre><p></span></span>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="html">The command <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bali-phy<span class="nt" style="color: navy;"></strong></span></span> and its associated tools should then be located in <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>~/Applications/bali-phy-3.<span class="idiff left right">1</span>/bin/<span class="nt" style="color: navy;"></code></span>. To install to another directory <span class="nt" style="color: navy;"><em</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"replaceable"</span><span class="nt" style="color: navy;">><code></span>dir<span class="nt" style="color: navy;"></code></em></span>, specify --prefix=<span class="nt" style="color: navy;"><em</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"replaceable"</span><span class="nt" style="color: navy;">><code></span>dir<span class="nt" style="color: navy;"></code></em></span> to <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>meson<span class="nt" style="color: navy;"></strong></span></span>.</span>

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="html">The command <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bali-phy<span class="nt" style="color: navy;"></strong></span></span> and its associated tools should then be located in <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>~/Applications/bali-phy-3.<span class="idiff left right">2</span>/bin/<span class="nt" style="color: navy;"></code></span>. To install to another directory <span class="nt" style="color: navy;"><em</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"replaceable"</span><span class="nt" style="color: navy;">><code></span>dir<span class="nt" style="color: navy;"></code></em></span>, specify --prefix=<span class="nt" style="color: navy;"><em</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"replaceable"</span><span class="nt" style="color: navy;">><code></span>dir<span class="nt" style="color: navy;"></code></em></span> to <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>meson<span class="nt" style="color: navy;"></strong></span></span>.</span>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="html">      <span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="html">    <span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="html">      <span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"section"</span><span class="nt" style="color: navy;">><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"titlepage"</span><span class="nt" style="color: navy;">><div><div><h3</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"idp26"</span><span class="nt" style="color: navy;">></a></span>3.3. Options: compiler and linker flags<span class="nt" style="color: navy;"></h3></div></div></div></span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="html"> </span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="html">      <span class="nt" style="color: navy;"><p></span>You can select the C++ compiler by setting the CXX variable.  A useful example of this is to use <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>g++-5<span class="nt" style="color: navy;"></strong></span></span> on systems where <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>g++<span class="nt" style="color: navy;"></strong></span></span> invokes a compiler that is too old:</span>

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<pre style="margin: 0;">-<span id="LC380" class="line" lang="html"> <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>CXX=g++-5 meson build --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">1</span><span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="html"> <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>CXX=g++-5 meson build --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">2</span><span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="html"> You may also set compiler and linker options using the CPPFLAGS, CXXFLAGS, and LDFLAGS variables.  For example, you can instruct the compiler to use all the features of your chip, instead of producing generic code that will run anywhere:</span>

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="html"> <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>CXXFLAGS="-mtune=native -march=native" meson --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">1</span><span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="html"> <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>CXXFLAGS="-mtune=native -march=native" meson --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">2</span><span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="html"> For example, you can set the CPPFLAGS and LDFLAGS variables to instruct the compiler where to look for libraries, such as cairo:</span>

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<td class="diff-line-num new_line old" data-linenumber="386" 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="LC385" class="line" lang="html">   <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>CPPFLAGS="-I/usr/local/include" LDFLAGS="-L/usr/local/lib" meson build --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">1</span><span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="html">   <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>CPPFLAGS="-I/usr/local/include" LDFLAGS="-L/usr/local/lib" meson build --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">2</span><span class="nt" style="color: navy;"></code></strong></pre><p></span></span>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="html"> Another useful example of this is to produce an OS X executable on that can run on older versions of OS X:</span>

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="html">   <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>CXXFLAGS="-mmacosx-version-min=10.9" LDFLAGS="-mmacosx-version-min=10.9" meson build --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">1</span><span class="nt" style="color: navy;"></code></strong></pre><p></span>  <span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="html">   <span class="nt" style="color: navy;"></p><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>CXXFLAGS="-mmacosx-version-min=10.9" LDFLAGS="-mmacosx-version-min=10.9" meson build --prefix=$HOME/Applications/bali-phy-3.<span class="idiff left right">2</span><span class="nt" style="color: navy;"></code></strong></pre><p></span>  <span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="html">      <span class="nt" style="color: navy;"></div></span></span>

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="html">    <span class="nt" style="color: navy;"></div></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">@@ -572,7 +573,7 @@ scale = 1,3:</pre><p></td>

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<pre style="margin: 0;"> <span id="LC573" class="line" lang="html">      executables and extracted them in the</span>

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<pre style="margin: 0;"> <span id="LC574" class="line" lang="html">      <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>~/Applications<span class="nt" style="color: navy;"></code></span> directory, then the</span>

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="html">      <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>examples/sequences/<span class="nt" style="color: navy;"></code></span> directory will be found at </span>

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<pre style="margin: 0;">-<span id="LC575" class="line" lang="html">      <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>~/Applications/bali-phy-3.<span class="idiff left right">1</span>/share/doc/bali-phy/examples/sequences/<span class="nt" style="color: navy;"></code></span>.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC576" class="line" lang="html">      <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"filename"</span><span class="nt" style="color: navy;">></span>~/Applications/bali-phy-3.<span class="idiff left right">2</span>/share/doc/bali-phy/examples/sequences/<span class="nt" style="color: navy;"></code></span>.</span>

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<pre style="margin: 0;"> <span id="LC577" class="line" lang="html">    <span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC578" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC579" class="line" lang="html">    <span class="nt" style="color: navy;"><p></span>Also note that <span class="nt" style="color: navy;"><span</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"command"</span><span class="nt" style="color: navy;">><strong></span>bali-phy<span class="nt" style="color: navy;"></strong></span></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">@@ -587,7 +588,7 @@ scale = 1,3:</pre><p></td>

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<pre style="margin: 0;"> <span id="LC588" class="line" lang="html">      </span>

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<pre style="margin: 0;"> <span id="LC589" class="line" lang="html">      <span class="nt" style="color: navy;"><p></span>Here we analyze the EF-Tu 5-taxon data set provided with</span>

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<pre style="margin: 0;"> <span id="LC590" class="line" lang="html"> the software.<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;">-<span id="LC590" class="line" lang="html">      <span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">></span> <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy ~/Applications/bali-phy-3.<span class="idiff left right">1</span>/share/doc/bali-phy/examples/sequences/EF-Tu/5d.fasta<span class="nt" style="color: navy;"></code></strong></pre></span></span>

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<pre style="margin: 0;">+<span id="LC591" class="line" lang="html">      <span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">></span> <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy ~/Applications/bali-phy-3.<span class="idiff left right">2</span>/share/doc/bali-phy/examples/sequences/EF-Tu/5d.fasta<span class="nt" style="color: navy;"></code></strong></pre></span></span>

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<pre style="margin: 0;"> <span id="LC592" class="line" lang="html">    <span class="nt" style="color: navy;"></div></div><br</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"example-break"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC593" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC594" class="line" lang="html">    <span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"example"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"idp779"</span><span class="nt" style="color: navy;">></a><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: navy;">><b></span>Example 2. Multiple-Rate Substitution Model<span class="nt" style="color: navy;"></b></p><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"example-contents"</span><span class="nt" style="color: navy;">></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">@@ -597,7 +598,7 @@ scale = 1,3:</pre><p></td>

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<pre style="margin: 0;"> <span id="LC598" class="line" lang="html"> invariant sites.  The amount of rate variation and the fraction of</span>

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<pre style="margin: 0;"> <span id="LC599" class="line" lang="html"> invariant sites are estimated<span class="nt" style="color: navy;"></p></span></span>

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<pre style="margin: 0;"> <span id="LC600" class="line" lang="html">      </span>

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<pre style="margin: 0;">-<span id="LC600" class="line" lang="html">      <span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">></span> <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy ~/Applications/bali-phy-3.<span class="idiff left right">1</span>/share/doc/bali-phy/examples/sequences/EF-Tu/5d.fasta --smodel lg08+Rates.log_normal+inv<span class="nt" style="color: navy;"></code></strong></pre></div></div><br</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"example-break"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">+<span id="LC601" class="line" lang="html">      <span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">></span> <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy ~/Applications/bali-phy-3.<span class="idiff left right">2</span>/share/doc/bali-phy/examples/sequences/EF-Tu/5d.fasta --smodel lg08+Rates.log_normal+inv<span class="nt" style="color: navy;"></code></strong></pre></div></div><br</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"example-break"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC602" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC603" class="line" lang="html">    <span class="nt" style="color: navy;"><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"example"</span><span class="nt" style="color: navy;">><a</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"idp787"</span><span class="nt" style="color: navy;">></a><p</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"title"</span><span class="nt" style="color: navy;">><b></span>Example 3. Fixed alignment<span class="nt" style="color: navy;"></b></p><div</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"example-contents"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="html">      </span>

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<pre style="margin: 0;"> <span id="LC606" class="line" lang="html">      the software. The <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>-Inone<span class="nt" style="color: navy;"></code></strong></span> option is used, fixing the alignment and making indels non-informative.</span>

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<pre style="margin: 0;"> <span id="LC607" class="line" lang="html">      <span class="nt" style="color: navy;"></p></span> </span>

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<pre style="margin: 0;">-<span id="LC608" class="line" lang="html">      <span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">></span> <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy ~/Applications/bali-phy-3.<span class="idiff left right">1</span>/share/doc/bali-phy/examples/sequences/5S-rRNA/25-muscle.fasta -Inone<span class="nt" style="color: navy;"></code></strong></pre></span></span>

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<pre style="margin: 0;">+<span id="LC609" class="line" lang="html">      <span class="nt" style="color: navy;"><pre</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"screen"</span><span class="nt" style="color: navy;">></span> <span class="nt" style="color: navy;"><code</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"prompt"</span><span class="nt" style="color: navy;">></span>%<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><strong</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"userinput"</span><span class="nt" style="color: navy;">><code></span>bali-phy ~/Applications/bali-phy-3.<span class="idiff left right">2</span>/share/doc/bali-phy/examples/sequences/5S-rRNA/25-muscle.fasta -Inone<span class="nt" style="color: navy;"></code></strong></pre></span></span>

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<pre style="margin: 0;"> <span id="LC610" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC611" class="line" lang="html">    <span class="nt" style="color: navy;"></div></div><br</span> <span class="na" style="color: teal;">class=</span><span class="s" style="color: #d14;">"example-break"</span><span class="nt" style="color: navy;">></span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!ENTITY  version        "3.<span class="idiff left right">1.4</span>"         ></span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!ENTITY  version        "3.<span class="idiff left right">2</span>"         ></span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!ENTITY  source.file    "bali-phy-&version;.tar.gz"         ></span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><!ENTITY  linux64.file   "bali-phy-&version;-linux64.tar.gz"         ></span></span>

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<pre style="margin: 0;"> <span id="LC849" class="line" lang="xml">  <span class="nt" style="color: navy;"></varlistentry></span></span>

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<pre style="margin: 0;"> <span id="LC850" class="line" lang="xml">  </span>

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<pre style="margin: 0;">+<span id="LC851" class="line" lang="xml">  <span class="nt" style="color: navy;"><varlistentry></span></span>

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<pre style="margin: 0;">+<span id="LC852" class="line" lang="xml">    <span class="nt" style="color: navy;"><term></span>C1.run.json<span class="nt" style="color: navy;"></term></span></span>

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<pre style="margin: 0;">+<span id="LC853" class="line" lang="xml">    <span class="nt" style="color: navy;"><listitem></span></span>

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<pre style="margin: 0;">+<span id="LC854" class="line" lang="xml">      <span class="nt" style="color: navy;"><para></span>JSON file containing information about the command line, models, hostname, start time, etc.<span class="nt" style="color: navy;"></para></span></span>

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<pre style="margin: 0;">+<span id="LC855" class="line" lang="xml">    <span class="nt" style="color: navy;"></listitem></span></span>

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<pre style="margin: 0;">+<span id="LC856" class="line" lang="xml">  <span class="nt" style="color: navy;"></varlistentry></span></span>

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<pre style="margin: 0;">+<span id="LC857" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC858" class="line" lang="xml">      <span class="nt" style="color: navy;"></variablelist></span></span>

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<pre style="margin: 0;"> <span id="LC859" class="line" lang="xml">      </span>

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<pre style="margin: 0;"> <span id="LC860" class="line" lang="xml">      <span class="nt" style="color: navy;"><para></span>For the last two files, each line in these files corresponds to one iteration.<span class="nt" style="color: navy;"></para></span></span>

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<br>

</li>

<li id="81ea4a51a393287db60c435548408876ef34189e">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#81ea4a51a393287db60c435548408876ef34189e"><strong>doc/README.pdf</strong></a>

<hr>

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<li id="3439b2366791301eeb9f98394b5f7740fba15089">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#3439b2366791301eeb9f98394b5f7740fba15089"><strong>doc/README.xhtml</strong></a>

The diff for this file was not included because it is too large.

<br>

</li>

<li id="e125d275f37ec5a578f0297c3809f0ee90f9172b">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#e125d275f37ec5a578f0297c3809f0ee90f9172b"><strong>examples/models/CoalMine.hs</strong></a>

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1

</td>

<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="haskell"><span class="kr" style="font-weight: 600;">module</span> <span class="nn" style="color: #555;"><span class="idiff left right">AirL</span>ine</span> <span class="kr" style="font-weight: 600;">where</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="haskell"><span class="kr" style="font-weight: 600;">module</span> <span class="nn" style="color: #555;"><span class="idiff left right">CoalM</span>ine</span> <span class="kr" style="font-weight: 600;">where</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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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="LC2" class="line" lang="haskell"><span class="kr" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">Distributions</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

</td>

<td class="diff-line-num new_line" data-linenumber="3" 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">

3

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="haskell"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line" data-linenumber="4" 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">

4

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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="LC4" class="line" lang="haskell"><span class="n" style="color: #333;">fatalities</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

</td>

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<br>

</li>

<li id="08026a676e400b8e8ff2249986683711897d9aa1">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#08026a676e400b8e8ff2249986683711897d9aa1"><strong>functions/rs07_relaxed_rates.json</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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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="LC1" class="line" lang="json"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

</td>

<td class="diff-line-num new_line" data-linenumber="2" 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">

2

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="s2" style="color: #d14;">"name"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"rs07_relaxed_rates"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

</td>

<td class="diff-line-num new_line" data-linenumber="3" 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">

3

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="s2" style="color: #d14;">"result_type"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"IndelModel"</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4" 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">

4

</td>

<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="s2" style="color: #d14;">"generate_function"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">false</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line" data-linenumber="4" 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">

4

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="s2" style="color: #d14;">"call"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"IModel.rs07_relaxed_rates_model"</span><span class="p">,</span></span>

</pre>

</td>

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6

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="s2" style="color: #d14;">"args"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">""</span><span class="p">,</span></span>

</pre>

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7

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;">    </span><span class="s2" style="color: #d14;">"extract"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"all"</span></span>

</pre>

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<br>

</li>

<li id="0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa"><strong>meson.build</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">project('bali-phy', ['cpp','c'],</span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">      version: '3.<span class="idiff left right">1.5</span>',</span>

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2

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">      version: '3.<span class="idiff left right">2</span>',</span>

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3

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">      default_options : [</span>

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4

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">        'buildtype=release',</span>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">        'cpp_std=c++14'</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="135" 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="135" 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">@@ -135,7 +135,7 @@ run_tests = find_program(join_paths(meson.source_root(),'tests/run-tests.py'))</td>

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135

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135

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="136" 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">

136

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136

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">test('bali-phy testsuite',</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" 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">

137

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<td class="diff-line-num new_line" data-linenumber="137" 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="LC137" class="line" lang="plaintext">     run_tests,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="138" 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">

138

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<td class="diff-line-num new_line old" data-linenumber="138" 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="LC138" class="line" lang="plaintext">     timeout: <span class="idiff left right">6</span>00,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="139" 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="LC138" class="line" lang="plaintext">     timeout: <span class="idiff left right">30</span>00,</span>

</pre>

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139

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">     workdir: join_paths(meson.source_root(),'tests'),</span>

</pre>

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140

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140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">     args:[baliphy.full_path(), packagepath])</span>

</pre>

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141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="146" 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="146" 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">@@ -146,7 +146,7 @@ testiphy = find_program(join_paths(meson.source_root(),'testiphy/testiphy'), req</td>

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<td class="diff-line-num old_line" data-linenumber="146" 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">

146

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext">if testiphy.found()</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="147" 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="LC147" class="line" lang="plaintext">  test('testiphy (likelihood testsuite)',</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="148" 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="LC148" class="line" lang="plaintext">       testiphy,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="149" 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">

149

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<td class="diff-line-num new_line old" data-linenumber="149" 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="LC149" class="line" lang="plaintext">       timeout: <span class="idiff left right">6</span>00,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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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<td class="diff-line-num new new_line" data-linenumber="149" 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">

149

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">       timeout: <span class="idiff left right">30</span>00,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" 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">

150

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext">       workdir: join_paths(meson.source_root(),'testiphy'),</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="151" 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">

151

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext">       args:[baliphy.full_path(), packagepath])</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" 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">

152

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext">endif</span></pre>

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<br>

</li>

<li id="084fd92134dca1a928080e561b8573277c2f7609">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#084fd92134dca1a928080e561b8573277c2f7609"><strong>scripts/bp-analyze</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="419" 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="419" 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">@@ -419,7 +419,13 @@ sub html_header</td>

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<td class="diff-line-num old_line" data-linenumber="419" 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">

419

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="420" 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="LC420" class="line" lang="html">      <span class="nc" style="color: #458; font-weight: 600;">.content</span> <span class="p">{</span><span class="nl">margin</span><span class="p">:</span><span class="m" style="color: #099;">1em</span><span class="p">;</span> <span class="nl">margin-top</span><span class="p">:</span> <span class="m" style="color: #099;">3em</span><span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="421" 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="421" 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">

421

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="html">      <span class="nc" style="color: #458; font-weight: 600;">.backlit</span> <span class="nt" style="color: navy;">td</span> <span class="p">{</span><span class="nl">background</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">rgb</span><span class="p">(</span><span class="m" style="color: #099;">220</span><span class="p">,</span><span class="m" style="color: #099;">220</span><span class="p">,</span><span class="m" style="color: #099;">220</span><span class="p">);}</span></span>

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<td class="diff-line-num new_line old" data-linenumber="422" 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="LC422" class="line" lang="html">      <span class="nc" style="color: #458; font-weight: 600;">.anchor</span> <span class="p">{</span><span class="nl">position</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">relative</span><span class="p">;</span> <span class="nl">top</span><span class="p">:</span> <span class="m" style="color: #099;">-3em</span><span class="p">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="423" 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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<td class="diff-line-num new new_line" data-linenumber="422" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC422" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="423" 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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<td class="diff-line-num new new_line" data-linenumber="423" 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="LC423" class="line" lang="html">      <span class="nd">:target:before</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="423" 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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<td class="diff-line-num new new_line" data-linenumber="424" 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="LC424" class="line" lang="html">        <span class="nl">content</span><span class="p">:</span><span class="s1" style="color: #d14;">""</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="423" 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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<td class="diff-line-num new new_line" data-linenumber="425" 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">

425

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC425" class="line" lang="html">        <span class="nl">display</span><span class="p">:</span><span class="nb" style="color: #0086b3;">block</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="423" 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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<td class="diff-line-num new new_line" data-linenumber="426" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC426" class="line" lang="html">        <span class="nl">height</span><span class="p">:</span><span class="m" style="color: #099;">2em</span><span class="p">;</span> <span class="c" style="color: #998; font-style: italic;">/* fixed header height*/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="423" 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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<td class="diff-line-num new new_line" data-linenumber="427" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC427" class="line" lang="html">        <span class="nl">margin</span><span class="p">:</span><span class="m" style="color: #099;">-2em</span> <span class="m" style="color: #099;">0</span> <span class="m" style="color: #099;">0</span><span class="p">;</span> <span class="c" style="color: #998; font-style: italic;">/* negative fixed header height */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="html">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="429" 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="LC429" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="html">      <span class="nt" style="color: navy;">h1</span> <span class="p">{</span><span class="nl">font-size</span><span class="p">:</span> <span class="m" style="color: #099;">150%</span><span class="p">;}</span></span>

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<td class="diff-line-num old_line" data-linenumber="425" 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="431" 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">

431

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="html">      <span class="nt" style="color: navy;">h2</span> <span class="p">{</span><span class="nl">font-size</span><span class="p">:</span> <span class="m" style="color: #099;">130%</span><span class="p">;</span> <span class="nl">margin-top</span><span class="p">:</span><span class="m" style="color: #099;">2.5em</span><span class="p">;</span> <span class="nl">margin-bottom</span><span class="p">:</span> <span class="m" style="color: #099;">1em</span><span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="7737234f8646445ec91cc3054366c218c54c92d8">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#7737234f8646445ec91cc3054366c218c54c92d8"><strong>src/builtins/Distribution.cc</strong></a>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma clang diagnostic ignored "-Wreturn-type-c-linkage"</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#undef NDEBUG</span></span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <valarray></span></span>

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>

</pre>

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<br>

</li>

<li id="b4eb2415f36da696dfb3e0536b3eca86a947ff5b">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#b4eb2415f36da696dfb3e0536b3eca86a947ff5b"><strong>src/builtins/SMC.cc</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="30" 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">@@ -30,7 +30,7 @@ double quantile(double eta, double p)</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">get_bin_boundaries</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">coalescent_rates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">level_boundaries</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="p">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="33" 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="LC33" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">coalescent_rates</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 class="idiff left">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">level_boundaries</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="34" 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="LC33" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">coalescent_rates</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="n" style="color: #333;">level_boundaries</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">level_boundaries</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="mf" style="color: #099;">0.0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" 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="35" 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="LC35" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" 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">

36

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<td class="diff-line-num new_line" data-linenumber="36" 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="LC36" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">b</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" 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="58" 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">@@ -58,13 +58,14 @@ vector<double> get_bin_boundaries(int n, const vector<double>& coalescent_rates,</td>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp">       <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">level_boundaries</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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59

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59

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" 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="LC60" class="line" lang="cpp">       <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delta_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quantile</span><span class="p">(</span><span class="n" style="color: #333;">coalescent_rates</span><span class="p">[</span><span class="n" style="color: #333;">level</span><span class="p">],</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">q2</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp">       <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delta_t</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">level_boundaries</span><span class="p">[</span><span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="62" 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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<td class="diff-line-num new new_line" data-linenumber="61" 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="LC61" class="line" lang="cpp">       <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delta_t</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">level_boundaries</span><span class="p">[</span><span class="n" style="color: #333;">level</span><span class="p"><span class="idiff left">]</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">level</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">level_boundaries</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp">       <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="63" 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="LC63" class="line" lang="cpp">           <span class="n" style="color: #333;">b</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delta_t</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" 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="64" 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="LC64" class="line" lang="cpp">           <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp">       <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" 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="66" 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="LC66" class="line" lang="cpp">       <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" 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="LC67" class="line" lang="cpp">       <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="68" 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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<td class="diff-line-num new new_line" data-linenumber="68" 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="LC68" class="line" lang="cpp">           <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">level_boundaries</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp">           <span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">level_boundaries</span><span class="p">[</span><span class="n" style="color: #333;">level</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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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp">           <span class="n" style="color: #333;">delta_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">level_boundaries</span><span class="p">[</span><span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">level_boundaries</span><span class="p">[</span><span class="n" style="color: #333;">level</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="71" 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="LC71" class="line" lang="cpp">           <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">delta_t</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="397" 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="398" 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">@@ -397,11 +398,13 @@ constexpr double scale_min = 1.0/scale_factor;</td>

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398

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">log_scale_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">177.445678223345999210811423093293201427328034396225345054e0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="399" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="399" 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="400" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="400" 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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<td class="diff-line-num new_line old" data-linenumber="401" 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="LC400" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">site_t</span> <span class="p">{</span><span class="n" style="color: #333;">unknown</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;">poly</span><span class="p">,</span><span class="n" style="color: #333;">mono</span><span class="p">,</span><span class="n" style="color: #333;">missing</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="401" 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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<td class="diff-line-num new new_line" data-linenumber="401" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">site_t</span> <span class="p">{</span><span class="n" style="color: #333;">unknown</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;">poly</span><span class="p">,</span><span class="n" style="color: #333;">mono</span><span class="p">,</span><span class="n" style="color: #333;">missing</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">empty</span></span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="402" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="402" 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="403" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">site_t</span> <span class="nf" style="color: #900; font-weight: 600;">classify_site</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="404" 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">

404

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="404" 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">

404

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<td class="diff-line-num new_line old" data-linenumber="405" 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="LC404" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span> <span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="405" 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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<td class="diff-line-num new new_line" data-linenumber="405" 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="LC405" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x1</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="n" style="color: #333;">and</span> <span class="n" style="color: #333;">x2</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="405" 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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<td class="diff-line-num new new_line" data-linenumber="406" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">site_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">empty</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="405" 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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<td class="diff-line-num new new_line" data-linenumber="407" 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="LC407" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span> <span class="n" style="color: #333;">x2</span><span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="408" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">site_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">missing</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="409" 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="LC409" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="410" 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="LC410" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">site_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mono</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="486" 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="489" 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">@@ -486,7 +489,12 @@ vector<pair<int,site_t>> classify_sites(const alignment& A)</td>

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<td class="diff-line-num new_line" data-linenumber="489" 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="LC489" 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;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="n" style="color: #333;">site_t</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sites</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="490" 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="LC490" 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;">int</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();)</span></span>

</pre>

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488

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<td class="diff-line-num new_line" data-linenumber="491" 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">

491

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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="LC491" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="489" 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">

489

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<td class="diff-line-num new_line old" data-linenumber="492" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC489" class="line" lang="cpp">  <span class="n" style="color: #333;">site_t</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">classify_site</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">A</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="490" 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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<td class="diff-line-num new new_line" data-linenumber="492" 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">

492

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp">  <span class="n" style="color: #333;">site_t</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">classify_site</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">A</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="490" 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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<td class="diff-line-num new new_line" data-linenumber="493" 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">

493

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">site_t</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">empty</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="490" 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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<td class="diff-line-num new new_line" data-linenumber="494" 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">

494

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="490" 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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<td class="diff-line-num new new_line" data-linenumber="495" 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">

495

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp">      <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="490" 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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<td class="diff-line-num new new_line" data-linenumber="496" 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">

496

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="490" 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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<td class="diff-line-num new new_line" data-linenumber="497" 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">

497

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="490" 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">

490

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<td class="diff-line-num new_line" data-linenumber="498" 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">

498

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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="LC498" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="491" 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">

491

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<td class="diff-line-num new_line" data-linenumber="499" 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">

499

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="492" 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">

492

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<td class="diff-line-num new_line" data-linenumber="500" 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">

500

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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="LC500" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">do</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="518" 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="526" 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">@@ -518,7 +526,9 @@ void smc_group(vector<double>& L, vector<double>& L2, int& scale, const vector<E</td>

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<td class="diff-line-num new_line" data-linenumber="526" 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">

526

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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="LC526" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="519" 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">

519

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<td class="diff-line-num new_line" data-linenumber="527" 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">

527

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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="LC527" 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;">int</span> <span class="n" style="color: #333;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n_bins</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="520" 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">

520

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<td class="diff-line-num new_line" data-linenumber="528" 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">

528

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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp">          <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">L</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="521" 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">

521

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<td class="diff-line-num new_line old" data-linenumber="529" 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="LC521" class="line" lang="cpp">      <span class="n" style="color: #333;">L2</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="522" 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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<td class="diff-line-num new new_line" data-linenumber="529" 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">

529

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="530" 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">

530

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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp">      <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0e-9</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="531" 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">

531

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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp">      <span class="n" style="color: #333;">L2</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>

</pre>

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522

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<td class="diff-line-num new_line" data-linenumber="532" 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">

532

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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523

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<td class="diff-line-num new_line" data-linenumber="533" 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">

533

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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp">  <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">taking</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="524" 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">

524

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<td class="diff-line-num new_line" data-linenumber="534" 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">

534

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="532" 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="542" 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">@@ -532,7 +542,7 @@ void smc_group(vector<double>& L, vector<double>& L2, int& scale, const vector<E</td>

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532

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp"></span>

</pre>

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533

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<td class="diff-line-num new_line" data-linenumber="543" 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="LC543" class="line" lang="cpp"><span class="n" style="color: #333;">log_double_t</span> <span class="n" style="color: #333;">smc</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rho_over_theta</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">coalescent_rates</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">level_boundaries</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">A</span><span class="p">)</span></span>

</pre>

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534

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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535

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<td class="diff-line-num new_line old" data-linenumber="545" 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="LC535" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">level_boundaries</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;"><span class="idiff left right">2</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="536" 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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<td class="diff-line-num new new_line" data-linenumber="545" 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="LC545" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">level_boundaries</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;"><span class="idiff left right">1</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="536" 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">

536

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<td class="diff-line-num new_line" data-linenumber="546" 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">

546

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">level_boundaries</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="mf" style="color: #099;">0.0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="537" 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">

537

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<td class="diff-line-num new_line" data-linenumber="547" 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">

547

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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="538" 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">

538

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<td class="diff-line-num new_line" data-linenumber="548" 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">

548

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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">rho_over_theta</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="564" 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="574" 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">@@ -564,8 +574,13 @@ log_double_t smc(double rho_over_theta, vector<double> coalescent_rates, vector<</td>

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<td class="diff-line-num old_line" data-linenumber="564" 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">

564

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<td class="diff-line-num new_line" data-linenumber="574" 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">

574

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<pre style="margin: 0;"> <span id="LC574" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="565" 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">

565

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<td class="diff-line-num new_line" data-linenumber="575" 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">

575

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="566" 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">

566

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<td class="diff-line-num new_line" data-linenumber="576" 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">

576

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<pre style="margin: 0;"> <span id="LC576" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// FIXME: I think we should be able to start at site -1 with L[i] = pi[i], if pi[i] is the equilibrium of T(j,k)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//        Its not exactly the equilibrium, so this is approximate, I guess.</span></span>

</pre>

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567

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<td class="diff-line-num new_line" data-linenumber="578" 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">

578

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<pre style="margin: 0;"> <span id="LC578" 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;">int</span> <span class="n" style="color: #333;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n_bins</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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568

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<td class="diff-line-num new_line old" data-linenumber="579" 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="LC568" class="line" lang="cpp">  <span class="n" style="color: #333;">L</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pi</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">emission_probabilities</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">](</span><span class="n" style="color: #333;">A</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">A</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="579" 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="LC579" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="580" 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">

580

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp">  <span class="n" style="color: #333;">L</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pi</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="581" 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="LC581" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//    if (A(0,0) >= 0 and A(0,1) >= 0)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="582" 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="LC582" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//        L[i] *= emission_probabilities[i](A(0,0), A(0,1));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="583" 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">

583

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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569

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<td class="diff-line-num new_line" data-linenumber="584" 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">

584

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<pre style="margin: 0;"> <span id="LC584" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="570" 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">

570

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<td class="diff-line-num new_line" data-linenumber="585" 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="LC585" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// # Iteratively compute likelihoods for remaining columns</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="571" 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="586" 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="LC586" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">transition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_transition_probabilities</span><span class="p">(</span><span class="n" style="color: #333;">bin_boundaries</span><span class="p">,</span> <span class="n" style="color: #333;">bin_times</span><span class="p">,</span> <span class="n" style="color: #333;">theta</span><span class="p">,</span> <span class="n" style="color: #333;">rho</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="610" 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="625" 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">@@ -610,7 +625,6 @@ extern "C" closure builtin_function_smc_density(OperationArgs& Args)</td>

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<td class="diff-line-num new_line" data-linenumber="625" 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="LC625" class="line" lang="cpp">    <span class="n" style="color: #333;">level_boundaries</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="626" 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="LC626" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">level_boundaries_</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="612" 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">

612

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<td class="diff-line-num new_line" data-linenumber="627" 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">

627

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<pre style="margin: 0;"> <span id="LC627" class="line" lang="cpp">  <span class="n" style="color: #333;">level_boundaries</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">as_double</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="613" 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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<td class="diff-line-num new_line old" data-linenumber="628" 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="LC613" class="line" lang="cpp">    <span class="n" style="color: #333;">level_boundaries</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="mi" style="color: #099;">100000</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Args</span><span class="p">.</span><span class="n" style="color: #333;">evaluate</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">);</span></span>

</pre>

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616

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630

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<pre style="margin: 0;"> <span id="LC630" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">A</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">as_</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

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<br>

</li>

<li id="5658f2b4f3a4f6cfedcbe6182ff69ec8c818ff46">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#5658f2b4f3a4f6cfedcbe6182ff69ec8c818ff46"><strong>src/mcmc/sample-two-nodes.cc</strong></a>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#undef NDEBUG</span></span>

</pre>

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2

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<td class="diff-line-num old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line" data-linenumber="2" 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="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">  Copyright (C) 2004-2007,2009-2014 Benjamin Redelings</span></span>

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4

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"></span>

</pre>

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</li>

<li id="cee142ff88dc5968288cf8e6adf24f1cf67facdf">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#cee142ff88dc5968288cf8e6adf24f1cf67facdf"><strong>src/models/rules.cc</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="167" 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="167" 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">@@ -167,11 +167,6 @@ ptree convert_rule(const Rules& R, Rule rule)</td>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp">  <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp">      <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alphabet</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">R</span><span class="p">,</span> <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_value</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="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">applied_args</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">get_child_optional</span><span class="p">(</span><span class="s" style="color: #d14;">"applied_args"</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="172" 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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<td class="diff-line-num new_line old" data-linenumber="170" 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="LC172" class="line" lang="cpp">  <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="173" 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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<td class="diff-line-num new_line old" data-linenumber="170" 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="LC173" class="line" lang="cpp">      <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">applied_args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_type</span><span class="p">(</span><span class="n" style="color: #333;">applied_args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_value</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="p">());</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="174" 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="LC174" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" 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="LC171" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rule</span><span class="p">;</span></span>

</pre>

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</li>

<li id="94c1320ff59df5a7dbd1f999929b578c570fd365">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#94c1320ff59df5a7dbd1f999929b578c570fd365"><strong>src/models/setup.cc</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -287,11 +287,6 @@ expression_ref arg_to_apply(const ptree& expression)</td>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">E</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp"><span class="n" style="color: #333;">expression_ref</span> <span class="n" style="color: #333;">apply_args</span><span class="p">(</span><span class="n" style="color: #333;">expression_ref</span> <span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ptree</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">applied_args</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="n" style="color: #333;">arg_to_apply</span><span class="p">(</span><span class="n" style="color: #333;">applied_args</span><span class="p">)};</span></span>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"><span class="n" style="color: #333;">optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">get_frequencies_from_tree</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ptree</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">model_rep</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">a</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pi</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">@@ -442,7 +437,6 @@ expression_ref get_model_as(const Rules& R, const ptree& model_rep, const map<st</td>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"call"</span><span class="p">))</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">myexception</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"No call for '"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"'"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// 6a. Extract parts of the rule</span></span>

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<pre style="margin: 0;">-<span id="LC445" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">generate_function</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"generate_function"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">perform_function</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"perform"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp">    <span class="n" style="color: #333;">ptree</span> <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_child</span><span class="p">(</span><span class="s" style="color: #d14;">"call"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="cpp">    <span class="n" style="color: #333;">ptree</span> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_child</span><span class="p">(</span><span class="s" style="color: #d14;">"args"</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="451" 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">@@ -451,20 +445,6 @@ expression_ref get_model_as(const Rules& R, const ptree& model_rep, const map<st</td>

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">myexception</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"For rule '"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"', function '"</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">call</span><span class="p">.</span><span class="n" style="color: #333;">get_value</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="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"' must be a qualified symbol or a builtin constructor like '(,)', but it is neither!"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cpp">    <span class="n" style="color: #333;">expression_ref</span> <span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dummy</span><span class="p">(</span><span class="n" style="color: #333;">call</span><span class="p">.</span><span class="n" style="color: #333;">get_value</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="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC454" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// This means (i) don't perform the arguments first and (ii) don't add "return" to the result.</span></span>

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<pre style="margin: 0;">-<span id="LC455" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">generate_function</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC456" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC457" 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;">int</span> <span class="n" style="color: #333;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">call</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp">  <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC459" class="line" lang="cpp">      <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">arg_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">array_index</span><span class="p">(</span><span class="n" style="color: #333;">call</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">get_value</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="p">();</span></span>

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<pre style="margin: 0;">-<span id="LC460" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// check that arg_name is a valid argument</span></span>

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<pre style="margin: 0;">-<span id="LC461" class="line" lang="cpp">      <span class="n" style="color: #333;">get_arg</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rule</span><span class="p">,</span> <span class="n" style="color: #333;">arg_name</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC462" class="line" lang="cpp">      <span class="n" style="color: #333;">expression_ref</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_model_as</span><span class="p">(</span><span class="n" style="color: #333;">R</span><span class="p">,</span> <span class="n" style="color: #333;">model_rep</span><span class="p">.</span><span class="n" style="color: #333;">get_child</span><span class="p">(</span><span class="n" style="color: #333;">arg_name</span><span class="p">),</span> <span class="n" style="color: #333;">scope</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC463" class="line" lang="cpp">      <span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">E</span><span class="p">,</span><span class="n" style="color: #333;">arg</span><span class="p">};</span></span>

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<pre style="margin: 0;">-<span id="LC464" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC465" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">E</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC466" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC467" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// 6b. Apply the arguments listed in the call : 'f call.name1 call.name2 call.name3'</span></span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//    There could be fewer of these than the rule arguments.</span></span>

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<pre style="margin: 0;"> <span id="LC450" 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;">int</span> <span class="n" style="color: #333;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">call</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="489" 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">@@ -489,11 +469,6 @@ expression_ref get_model_as(const Rules& R, const ptree& model_rep, const map<st</td>

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="cpp">  <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">arg_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argi</span><span class="p">.</span><span class="n" style="color: #333;">get_child</span><span class="p">(</span><span class="s" style="color: #d14;">"arg_name"</span><span class="p">).</span><span class="n" style="color: #333;">get_value</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="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="cpp">  <span class="n" style="color: #333;">expression_ref</span> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_model_as</span><span class="p">(</span><span class="n" style="color: #333;">R</span><span class="p">,</span> <span class="n" style="color: #333;">model_rep</span><span class="p">.</span><span class="n" style="color: #333;">get_child</span><span class="p">(</span><span class="n" style="color: #333;">arg_name</span><span class="p">),</span> <span class="n" style="color: #333;">extend_scope</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rule</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">scope</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC492" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Apply arguments if necessary</span></span>

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<pre style="margin: 0;">-<span id="LC493" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">applied_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argi</span><span class="p">.</span><span class="n" style="color: #333;">get_child_optional</span><span class="p">(</span><span class="s" style="color: #d14;">"applied_args"</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC494" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">applied_args</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="495" 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="LC495" class="line" lang="cpp">      <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">apply_args</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">applied_args</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC496" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">log_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">arg_name</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Prefix "arg_name" (arg_+arg_name)</span></span>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp">  <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">Prefix</span><span class="p">,</span> <span class="n" style="color: #333;">log_name</span><span class="p">,</span> <span class="n" style="color: #333;">arg</span><span class="p">};</span></span>

</pre>

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<br>

</li>

<li id="904995394c50a686a92b0e3e3164e7b530b14385">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#904995394c50a686a92b0e3e3164e7b530b14385"><strong>src/tools/alignment-compare.cc</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" 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="34" 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">@@ -34,10 +34,6 @@ along with BAli-Phy; see the file COPYING.  If not see</td>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "distance-methods.H"</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "rng.H"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef NDEBUG</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#undef NDEBUG</span></span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/program_options.hpp></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/shared_ptr.hpp></span></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "io.H"</span></span>

</pre>

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<br>

</li>

<li id="f309b9d7792dc999516170b579b783e20b312e55">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#f309b9d7792dc999516170b579b783e20b312e55"><strong>src/tools/alignment-identity.cc</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="56" 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">@@ -56,8 +56,6 @@ void do_setup(const variables_map& args,vector<alignment>& alignments)</td>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">myexception</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Alignment sample is empty."</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#undef NDEBUG</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">n_with_identity</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">A</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s1</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s2</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">I</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Get matches</span></span>

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<br>

</li>

<li id="d6a2673b0c73795d4dd427b89696a0ff5bd3c84e">

<a href="https://salsa.debian.org/med-team/bali-phy/compare/ee79a02e55d7c1b0dcddf63ff96c2dd1e5dc4cac...a40d3759c24095072e4481ced05d83543aada7c5#d6a2673b0c73795d4dd427b89696a0ff5bd3c84e"><strong>src/tools/alignment-smc.cc</strong></a>

<hr>

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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">@@ -278,8 +278,10 @@ bool is_masked_column(const alignment& A, int c)</td>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">is_variant_column</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">c</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l0</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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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">n_sequences</span><span class="p">()</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">l0</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;">i</span><span class="o" style="font-weight: 600;">++</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">@@ -291,6 +293,15 @@ bool is_variant_column(const alignment& A, int c)</td>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count_variant_columns</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c2</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC299" 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;">int</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">c1</span><span class="p">;</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">c2</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_variant_column</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,</span><span class="n" style="color: #333;">c</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp">      <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">remove_columns</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">function</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">remove</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="575" 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">@@ -575,31 +586,60 @@ void write_histogram(std::ostream& o, int blocksize, const alignment& A)</td>

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<pre style="margin: 0;"> <span id="LC586" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC587" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC588" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="578" 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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<td class="diff-line-num new_line old" data-linenumber="589" 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="LC578" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// The counts should be Poisson distributed.  It will be relatively ra<span class="idiff left right">t</span>e to get</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// The counts should be Poisson distributed.  It will be relatively ra<span class="idiff left right">r</span>e to get</span></span>

</pre>

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590

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<pre style="margin: 0;"> <span id="LC590" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// counts more than 10 times higher than the mean</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="580" 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">

580

</td>

<td class="diff-line-num new_line" data-linenumber="591" 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">

591

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC591" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="581" 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">

581

</td>

<td class="diff-line-num new_line old" data-linenumber="592" 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="LC581" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// FIXME - this does depend on the window boundaries.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="582" 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">

582

</td>

<td class="diff-line-num new_line old" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC582" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Change so that we use a sliding window.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="592" 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">

592

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp"><span class="n" style="color: #333;">dynamic_bitset</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">block_mask</span><span class="p">(</span><span class="n" style="color: #333;">dynamic_bitset</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">blocksize</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="593" 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">

593

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="594" 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">

594

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">mask2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mask</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="595" 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">

595

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<pre style="margin: 0;">+<span id="LC595" 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;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">blocksize</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="596" 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">

596

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="597" 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">

597

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp">  <span class="n" style="color: #333;">mask2</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="598" 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">

598

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp">  <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">mask2</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="599" 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">

599

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="600" 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">

600

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mask</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="601" 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">

601

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="583" 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">

583

</td>

<td class="diff-line-num new_line" data-linenumber="602" 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">

602

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC602" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="584" 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">

584

</td>

<td class="diff-line-num new_line" data-linenumber="603" 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">

603

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC603" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">autoclean</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">A</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="585" 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">

585

</td>

<td class="diff-line-num new_line" data-linenumber="604" 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">

604

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC604" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="586" 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">

586

</td>

<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC586" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="605" 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">

605

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mean<span class="idiff left right">_snps_per_block</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="587" 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">

587

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<td class="diff-line-num new_line" data-linenumber="606" 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">

606

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC606" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">factor</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">10.0</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="588" 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">

588

</td>

<td class="diff-line-num new_line old" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC588" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left right">L</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="607" 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">

607

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left right">n_sites</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="589" 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">

589

</td>

<td class="diff-line-num new_line" data-linenumber="608" 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">

608

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC608" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">S</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_snps</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="590" 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">

590

</td>

<td class="diff-line-num new_line" data-linenumber="609" 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">

609

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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="LC609" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">S</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">myexception</span><span class="p">()</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Refusing to autoclean chromosome with < 100 variant sites."</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="591" 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">

591

</td>

<td class="diff-line-num new_line" data-linenumber="610" 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">

610

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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="LC610" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="592" 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">

592

</td>

<td class="diff-line-num new_line" data-linenumber="611" 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">

611

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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="LC611" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">masked</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="593" 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">

593

</td>

<td class="diff-line-num new_line old" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC593" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">blocksize</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">L</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">mean</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">S</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="594" 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">

594

</td>

<td class="diff-line-num new_line old" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC594" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">snps_in_blocks</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">blocksize</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="612" 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">

612

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">blocksize</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">n_sites</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">mean_snps_per_block</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">S</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="595" 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">

595

</td>

<td class="diff-line-num new_line" data-linenumber="613" 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">

613

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC613" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="596" 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">

596

</td>

<td class="diff-line-num new_line old" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC596" 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;">int</span> <span class="n" style="color: #333;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="597" 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">

597

</td>

<td class="diff-line-num new_line old" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC597" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">mean</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">factor</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="614" 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">

614

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp">    <span class="n" style="color: #333;">dynamic_bitset</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">mask</span><span class="p">(</span><span class="n" style="color: #333;">n_sites</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="615" 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">

615

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="616" 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">

616

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC616" 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;">int</span> <span class="n" style="color: #333;">c2</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;">c2</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n_sites</span><span class="p">;</span> <span class="n" style="color: #333;">c2</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="617" 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">

617

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="618" 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">

618

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">blocksize</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="619" 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">

619

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="620" 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">

620

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span>            <span class="n" style="color: #333;">is_variant_column</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,</span><span class="n" style="color: #333;">c2</span><span class="p">))</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="621" 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">

621

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">is_variant_column</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,</span><span class="n" style="color: #333;">c1</span><span class="p">))</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="622" 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">

622

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="623" 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">

623

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">count_variant_columns</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">c1</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">c2</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="624" 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">

624

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="625" 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">

625

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">mean_snps_per_block</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">factor</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="598" 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">

598

</td>

<td class="diff-line-num new_line" data-linenumber="626" 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">

626

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC626" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="627" 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">

627

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp">      <span class="n" style="color: #333;">mask</span><span class="p">.</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;">c2</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="599" 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">

599

</td>

<td class="diff-line-num new_line" data-linenumber="628" 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">

628

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp">      <span class="n" style="color: #333;">masked</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="600" 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">

600

</td>

<td class="diff-line-num new_line old" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC600" 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;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">blocksize</span><span class="p">;</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">blocksize</span><span class="p">;</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="601" 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">

601

</td>

<td class="diff-line-num new_line old" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC601" class="line" lang="cpp">          <span class="n" style="color: #333;">mask_column</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="602" 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">

602

</td>

<td class="diff-line-num new_line" data-linenumber="629" 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">

629

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC629" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="630" 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">

630

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="631" 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">

631

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">mask2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_mask</span><span class="p">(</span><span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="n" style="color: #333;">blocksize</span><span class="p">);</span></span>

</pre>

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633

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<pre style="margin: 0;">+<span id="LC633" 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;">int</span> <span class="n" style="color: #333;">i</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;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n_sites</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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634

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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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635

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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mask2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="636" 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">

636

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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp">      <span class="n" style="color: #333;">mask_column</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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639

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<pre style="margin: 0;">+<span id="LC639" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//    std::cerr<<"Masked "<<masked<<" sites\n";</span></span>

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<td class="diff-line-num new new_line" data-linenumber="642" 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="LC642" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC643" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">masked</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="645" 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="LC645" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="642" 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="682" 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">@@ -642,7 +682,9 @@ int main(int argc,char* argv[])</td>

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<pre style="margin: 0;"> <span id="LC682" class="line" lang="cpp"></span>

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683

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<pre style="margin: 0;"> <span id="LC683" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">A</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">A0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="684" 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="LC684" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">get_alphabet</span><span class="p">();</span></span>

</pre>

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC645" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="685" 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">

685

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="686" 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">

686

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"autoclean"</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="687" 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">

687

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp">      <span class="n" style="color: #333;">autoclean</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="646" 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">

646

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<td class="diff-line-num new_line" data-linenumber="688" 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">

688

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC688" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="647" 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">

647

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<td class="diff-line-num new_line" data-linenumber="689" 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">

689

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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="LC689" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"mask-file"</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="648" 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">

648

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<td class="diff-line-num new_line" data-linenumber="690" 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">

690

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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="LC690" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="653" 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="695" 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">@@ -653,15 +695,6 @@ int main(int argc,char* argv[])</td>

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<td class="diff-line-num old_line" data-linenumber="653" 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">

653

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<td class="diff-line-num new_line" data-linenumber="695" 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">

695

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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="LC695" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="654" 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">

654

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<td class="diff-line-num new_line" data-linenumber="696" 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">

696

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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="LC696" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="655" 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">

655

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<td class="diff-line-num new_line" data-linenumber="697" 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">

697

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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="LC697" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="656" 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">

656

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<td class="diff-line-num new_line old" data-linenumber="698" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC656" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"autoclean"</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="657" 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">

657

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<td class="diff-line-num new_line old" data-linenumber="698" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC657" class="line" lang="cpp">      <span class="n" style="color: #333;">autoclean</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="658" 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">

658

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<td class="diff-line-num new_line old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC658" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="659" 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">

659

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<td class="diff-line-num new_line old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC659" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"histogram"</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="660" 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">

660

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<td class="diff-line-num new_line old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC660" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="661" 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">

661

</td>

<td class="diff-line-num new_line old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC661" class="line" lang="cpp">      <span class="n" style="color: #333;">write_histogram</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="s" style="color: #d14;">"histogram"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span> <span class="n" style="color: #333;">A</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="662" 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">

662

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<td class="diff-line-num new_line old" data-linenumber="698" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC662" class="line" lang="cpp">      <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="663" 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">

663

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<td class="diff-line-num new_line old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC663" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="664" 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">

664

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<td class="diff-line-num new_line old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC664" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="665" 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">

665

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698

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<pre style="margin: 0;"> <span id="LC698" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"mask-gaps"</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="666" 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">

666

</td>

<td class="diff-line-num new_line" data-linenumber="699" 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">

699

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC699" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="667" 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">

667

</td>

<td class="diff-line-num new_line" data-linenumber="700" 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">

700

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC700" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// 1. label gap columns with 2 to remove them.</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="678" 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="711" 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">@@ -678,6 +711,12 @@ int main(int argc,char* argv[])</td>

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<td class="diff-line-num old_line" data-linenumber="678" 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">

678

</td>

<td class="diff-line-num new_line" data-linenumber="711" 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">

711

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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="LC711" class="line" lang="cpp">      <span class="n" style="color: #333;">remove_and_mask_columns</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gaps</span><span class="p">](</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">){</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gaps</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];});</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="679" 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">

679

</td>

<td class="diff-line-num new_line" data-linenumber="712" 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">

712

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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="LC712" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="680" 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">

680

</td>

<td class="diff-line-num new_line" data-linenumber="713" 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">

713

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC713" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="714" 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">

714

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"histogram"</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="715" 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">

715

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="716" 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">

716

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp">      <span class="n" style="color: #333;">write_histogram</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="s" style="color: #d14;">"histogram"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span> <span class="n" style="color: #333;">A</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="717" 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">

717

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp">      <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="718" 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">

718

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="719" 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">

719

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="681" 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">

681

</td>

<td class="diff-line-num new_line" data-linenumber="720" 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">

720

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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="LC720" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">//----- Count informative/non-constant sites ----//</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="682" 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">

682

</td>

<td class="diff-line-num new_line" data-linenumber="721" 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">

721

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC721" class="line" lang="cpp">  <span class="n" style="color: #333;">dynamic_bitset</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">informative</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="683" 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">

683

</td>

<td class="diff-line-num new_line" data-linenumber="722" 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">

722

</td>

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<pre style="margin: 0;"> <span id="LC722" class="line" lang="cpp">  <span class="n" style="color: #333;">dynamic_bitset</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">informative2</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>

</pre>

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