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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/fitgcp">Debian Med / fitgcp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/commit/9cb24d5538a7e5567b09592d889f9b9e581c2873">9cb24d55</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:56:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/commit/9060f655e8456d7ff1fc45ae963027ada9761183">9060f655</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:57:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Switch Build system to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/commit/4a05c6df1c64c3e7bd855c0d6af3a9aeb9c13d25">4a05c6df</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:58:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/commit/88f0db3e42835ba8147336d4a1cd688ad4d78b69">88f0db3e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:58:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/commit/dd371b68ca8e160d686331b643823da6b7708414">dd371b68</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:58:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in copyright format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/commit/0dd63d0d91fce2e7afc75ef3acd899bbfd8ee847">0dd63d0d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-10T06:59:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/fitgcp/compare/0fc0368e04b9adda48dc4cbb3f40873cfc8c91ce...0dd63d0d91fce2e7afc75ef3acd899bbfd8ee847#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fitgcp (0.0.20150429-3) unstable; urgency=medium</span>
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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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #936518</span>
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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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Secure URI in copyright format</span>
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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">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 10 Sep 2019 08:58:14 +0200</span>
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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">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(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="LC11" class="line" lang="plaintext">fitgcp (0.0.20150429-2) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * debhelper 11</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/fitgcp/compare/0fc0368e04b9adda48dc4cbb3f40873cfc8c91ce...0dd63d0d91fce2e7afc75ef3acd899bbfd8ee847#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<td class="diff-line-num old old_line" 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="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/fitgcp/compare/0fc0368e04b9adda48dc4cbb3f40873cfc8c91ce...0dd63d0d91fce2e7afc75ef3acd899bbfd8ee847#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python-pysam</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2</span>.0</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pysam</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.0</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/fitgcp</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/fitgcp.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: http://sourceforge.net/projects/fitgcp/</span>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -16,10 +16,10 @@ Package: fitgcp</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> python-scipy,</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> python-numpy,</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> python-pysam</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> ${python<span class="idiff left right">3</span>:Depends},</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-scipy,</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-numpy,</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-pysam</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Description: fitting genome coverage distributions with mixture models</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Genome coverage, the number of sequencing reads mapped to a position in</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> a genome, is an insightful indicator of irregularities within sequencing</span>
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<a href="https://salsa.debian.org/med-team/fitgcp/compare/0fc0368e04b9adda48dc4cbb3f40873cfc8c91ce...0dd63d0d91fce2e7afc75ef3acd899bbfd8ee847#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: fitGCP</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: Martin S. Lindner <LindnerM@rki.de></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: http://sourceforge.net/projects/fitgcp/files/</span>
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<a href="https://salsa.debian.org/med-team/fitgcp/compare/0fc0368e04b9adda48dc4cbb3f40873cfc8c91ce...0dd63d0d91fce2e7afc75ef3acd899bbfd8ee847#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/936518</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Tue, 10 Sep 2019 08:55:27 +0200</span></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">--- a/README.txt</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/README.txt</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Help on python script fitGCP.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Help on python3 script fitGCP.py</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> Fits mixtures of probability distributions to genome coverage profiles using an</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> EM-like iterative algorithm.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -25,7 +25,7 @@</span> USAGE:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> fitGCP runs on the command line. The following command describes the general</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> structure:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python fitGCP.py [options] NAME</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 fitGCP.py [options] NAME</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> fitGCP fits mixtures of probability distributions to genome coverage profiles using</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> an EM-like iterative algorithm.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -76,4 +76,4 @@</span> Options:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> distributions.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> -l, --log Enable logging. Default: False</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> --view Only view the GCP. Do not fit any distribution.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Respects cutoff (-c). Default: False</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</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;">+ Respects cutoff (-c). Default: False</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/fitGCP.py</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/fitGCP.py</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> Created on Fri Aug 31 2012 14:05</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -31,7 +31,7 @@</span> SOFTWARE, EVEN IF ADVISED OF THE POSSIBI</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> usage = """</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> %prog [options] NAME</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Help on python script fitGCP.py</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Help on python3 script fitGCP.py</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> Fits mixtures of probability distributions to genome coverage profiles using an</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> EM-like iterative algorithm.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span> import sys</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> import os</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> from collections import namedtuple</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> import time</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import cPickle</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pickle</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> from optparse import OptionParser</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> from scipy.special import digamma, betainc</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> from scipy.optimize import newton</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="p">@@ -136,7 +136,7 @@</span> class NBinom(Distribution):</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> if self._use_MOM:</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> if var < mean:</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Warning: var < mean"</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Warning: var < mean")</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> var = 1.01*mean</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> self._p1 = mean**2 / (var - mean)</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> self._p2 = mean / var</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -154,9 +154,9 @@</span> class NBinom(Distribution):</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> maxiter=10000)</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> self._p2 = (self._p1)/(self._p1+mean)</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> except:</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Warning: MLE for negative binomial failed. Using MOM."</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Warning: MLE for negative binomial failed. Using MOM.")</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> if var < mean:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Warning: var < mean"</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Warning: var < mean")</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> var = 1.01*mean</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> self._p1 = mean**2 / (var - mean)</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> self._p2 = mean / var</span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="p">@@ -216,7 +216,7 @@</span> class NbTail(TailDistribution):</span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> if isinstance(nbinom, NBinom):</span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> self._parent = nbinom</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise(Exception("NbTail must be connected to a NBinom object"))</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise Exception</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> def pmf(self, x):</span>
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<td class="diff-line-num new new_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> if np.isscalar(x) and x == 0:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="p">@@ -253,7 +253,7 @@</span> class PoissonTail(TailDistribution):</span>
</pre>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> if isinstance(poisson, Poisson):</span>
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<td class="diff-line-num new new_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> self._parent = poisson</span>
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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise(Exception("PoissonTail must be connected to a Poisson object"))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise Exception</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> def pmf(self, x):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> if self._p1 < 1.:</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="p">@@ -338,7 +338,7 @@</span> class DataSet:</span>
</pre>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> def read_from_pickle(self,filename):</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> """ read a genome coverage profile from a pickle file. """</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- data = cPickle.load(open(filename,'r'))</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ data = pickle.load(open(filename,'r'))</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> self.cov = np.array(data[0],dtype=np.int)</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> self.count = np.array(data[1],dtype=np.int)</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="p">@@ -375,7 +375,7 @@</span> class DataSet:</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> </span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> def write_to_pickle(self, filename):</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> """ store dataset in a pickle file. """</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return cPickle.dump([self.cov, self.count, self.rlen, self.rds,</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return pickle.dump([self.cov, self.count, self.rlen, self.rds,</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> self.glen, self.fname], open(filename,'w'))</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> </span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="p">@@ -471,7 +471,7 @@</span> class Logger:</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> def log(self, s, c=True):</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> """ write string s to log file and print to console (if c) """</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> if c:</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print s</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(s)</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> if self.log_file:</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> self.log_file.write(s+'\n')</span>
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<td class="diff-line-num new new_line" data-linenumber="121" 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">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="p">@@ -585,7 +585,7 @@</span> if __name__ == "__main__":</span>
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<td class="diff-line-num new new_line" data-linenumber="123" 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">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> # load data</span>
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<td class="diff-line-num new new_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> DS = DataSet()</span>
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> if os.path.exists(name+'.pcl'):</span>
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<td class="diff-line-num new new_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'found pickle file'</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('found pickle file')</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> DS.read_from_pickle(name+'.pcl')</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> else:</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> DS.read_from_sam(name+'.sam')</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="p">@@ -617,7 +617,7 @@</span> if __name__ == "__main__":</span>
</pre>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> # create empty mixture model</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> MM = np.array([])</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> create_plot(DS,MM,name+'.png')</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Wrote GCP plot to file %s."%(name+'.png')</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Wrote GCP plot to file %s."%(name+'.png'))</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> sys.exit(0)</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> </span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="p">@@ -710,7 +710,7 @@</span> if __name__ == "__main__":</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> # run the iteration, repeatedly update the variables MM and GAMMA</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> t_start = time.time()</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> for i,change,diff in iterative_fitting(DS, MM, GAMMA, options.steps): </span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print i</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(i)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> t_step = time.time() - t_start</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> lg.log(('step#: '+str(i+1)).ljust(20)+'time: '+str(round(t_step,1))+'s'</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> +'\n',False)</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="p">@@ -792,4 +792,4 @@</span> if __name__ == "__main__":</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> if plot:</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> create_plot(DS,MM,name+'_'+options.dist+'.png')</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\nFinished."</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\nFinished.")</span></span></pre>
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<a href="https://salsa.debian.org/med-team/fitgcp/compare/0fc0368e04b9adda48dc4cbb3f40873cfc8c91ce...0dd63d0d91fce2e7afc75ef3acd899bbfd8ee847#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/fitgcp/compare/0fc0368e04b9adda48dc4cbb3f40873cfc8c91ce...0dd63d0d91fce2e7afc75ef3acd899bbfd8ee847#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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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"># DH_VERBOSE := 1</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"></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">%:</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">3</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">override_dh_fixperms:</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh_fixperms</span>
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