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<h3>
Andreas Tille pushed to branch debian/jessie-backports
at <a href="https://salsa.debian.org/med-team/seaview">Debian Med / seaview</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seaview/commit/8880102e845038eb13eb6da4251332016e4515ca">8880102e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-02-01T10:14:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable reading number of bootstraps from phyml runs
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<li>
<strong><a href="https://salsa.debian.org/med-team/seaview/commit/ae372fca53428f43e98c2cc123d6c43f7663c3c0">ae372fca</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-02-01T12:55:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Close bug and upload
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/seaview/commit/ecdea44d1b0076cb8cebbc19638f623244fa8cd9">ecdea44d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-02-06T09:44:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into debian/jessie-backports
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<li>
<strong><a href="https://salsa.debian.org/med-team/seaview/commit/f8a5720bd5a0d4aa8bfe150c539a14ad412e215e">f8a5720b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2017-02-06T09:44:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rebuild for jessie-backports
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#9fd8d3a6e6c07809b68c644018a223b696ab85ac">
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+
debian/patches/evaluate_phyml_bootstrap_number.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/seaview/compare/9ecce4bc02051ab0d2c82f97a18c05f11f3c276a...f8a5720bd5a0d4aa8bfe150c539a14ad412e215e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">seaview (1:4.6.1.2-2~bpo8+1) jessie-backports; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Rebuild for jessie-backports.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 06 Feb 2017 09:44:39 +0100</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">seaview (1:4.6.1.2-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Enable reading number of bootstraps from phyml runs</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Closes: #853835</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 01 Feb 2017 12:54:56 +0100</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">seaview (1:4.6.1.2-1~bpo8+1) jessie-backports; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(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="LC16" class="line" lang="plaintext"> * Rebuild for jessie-backports to become compatible with backported phyml</span>
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<li id="9fd8d3a6e6c07809b68c644018a223b696ab85ac">
<a href="https://salsa.debian.org/med-team/seaview/compare/9ecce4bc02051ab0d2c82f97a18c05f11f3c276a...f8a5720bd5a0d4aa8bfe150c539a14ad412e215e#9fd8d3a6e6c07809b68c644018a223b696ab85ac"><strong>debian/patches/evaluate_phyml_bootstrap_number.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Enable reading number of bootstraps from phyml runs</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Author: Manolo Gouy <manolo.gouy@univ-lyon1.fr></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> Patch extracted from Upstream version 4.6.1.3</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Last-Update: Wed, 01 Feb 2017 08:51:09 +0100</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/trees.cxx</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/trees.cxx</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1201,6 +1201,24 @@ void run_phyml_callback(Fl_Widget *ob, v</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> display_tree = put_names_back_in_tree(display_tree, truenames);</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> //process bootstrap trees</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> char *bootstrap_trees = NULL;</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (replicates > 0) {</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sprintf(input, "%s.phy_phyml_boot_stats.txt", base_fname);</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ in = fopen(input, "r");</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (!in) {</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sprintf(input, "%s.phy_phyml_boot_stats", base_fname);</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ in = fopen(input, "r");</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (in) { // compute the true # of bootstrap replicates because parallelized phyML can compute a few more</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char line[150];</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while ((p = fgets(line, sizeof(line), in))) {</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while (*p == ' ') p++;</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (*p == '#') {</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sscanf(p+1, "%d", &replicates);</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fclose(in);</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> if (replicates > 0 && b_keep_trees->value()) {</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> sprintf(input, "%s.phy_phyml_boot_trees.txt", base_fname);</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> in = fopen(input, "r");</span></pre>
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<a href="https://salsa.debian.org/med-team/seaview/compare/9ecce4bc02051ab0d2c82f97a18c05f11f3c276a...f8a5720bd5a0d4aa8bfe150c539a14ad412e215e#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">evaluate_phyml_bootstrap_number.patch</span></pre>
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