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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/uc-echo">Debian Med / uc-echo</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/commit/09522c2052272812e5146e0f04257e23dbb09b0c">09522c20</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T19:22:57Z</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/uc-echo/commit/d28d92103a16f1b5c4b369badd39d5221268e72b">d28d9210</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T19:24:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/commit/72d8f4342e0c942e39c169a83d63b64bc0a0f5b0">72d8f434</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T19:24:25Z</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/uc-echo/commit/d34960aaa8c666071f1584347d9f22183fb20d0b">d34960aa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T19:24:27Z</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/uc-echo/commit/30577d24506f6fb4012a6f971e1cca866762d3b6">30577d24</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T19:24:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/commit/0530a984b4d217170ccf4845b46a001b74afe8b0">0530a984</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T19:24:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/commit/be81d21facf3e5c3a456c7304bd448e993fee45d">be81d21f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T19:24:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove trailing whitespace in debian/rules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/commit/a562c04aab263dd1f8e57e7794cd53c0ec2b8f1d">a562c04a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T19:24:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/commit/c0fc36f96f3d7cb0c91adef5c45da7da5a90b15f">c0fc36f9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T19:24:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure URI in debian/watch.
Fixes lintian: debian-watch-uses-insecure-uri
See https://lintian.debian.org/tags/debian-watch-uses-insecure-uri.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/uc-echo/commit/58584eacc2504c7657a3d1a4ea3a4c152ffe27d0">58584eac</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-02T19:25:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>8 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
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#47a651b586e42387ccdfca5a878d963be2a87da5">
debian/script/uc-echo
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/uc-echo/compare/1271416909837719c8dcc1204aa489ebebabc251...58584eacc2504c7657a3d1a4ea3a4c152ffe27d0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">uc-echo (1.12-12) 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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * 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: #938741</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"> * Remove trailing whitespace in debian/changelog</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"> * Remove trailing whitespace in debian/control</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"> * Remove trailing whitespace in debian/rules</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"> * Trim trailing whitespace.</span>
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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">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Use secure URI in debian/watch.</span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"></span>
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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">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 02 Sep 2019 21:24:31 +0200</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">uc-echo (1.12-11) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" 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="103" 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">@@ -89,7 +103,7 @@ uc-echo (1.12-2) unstable; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> * debian/control: use g++-multilib only when available (Closes: #727657)</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"> * debian/control: use canonical vcs-fields</span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"> * add patch to compile on mips/mipsel<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> * add patch to compile on mips/mipsel</span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> -- Thorsten Alteholz <debian@alteholz.de> Tue, 29 Oct 2013 19:00:07 +0100</span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" 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="112" 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">@@ -98,4 +112,3 @@ uc-echo (1.12-1) unstable; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext"> * initial version (Closes: #704902)</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"> -- Thorsten Alteholz <debian@alteholz.de> Tue, 12 Mar 2013 18:00:07 +0100</span></pre>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"></span></pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/uc-echo/compare/1271416909837719c8dcc1204aa489ebebabc251...58584eacc2504c7657a3d1a4ea3a4c152ffe27d0#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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1
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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/uc-echo/compare/1271416909837719c8dcc1204aa489ebebabc251...58584eacc2504c7657a3d1a4ea3a4c152ffe27d0#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -5,13 +5,12 @@ Uploaders: Thorsten Alteholz <debian@alteholz.de>,</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Navid Fehrenbacher <nf@q-leap.de></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python-all-dev:any,</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> libpython-all-dev,</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python-scipy:native,</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> python-numpy:native,</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3-all-dev:any,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-scipy:native,</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3-numpy:native,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> g++-multilib [i386 powerpc sparc x32]</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3</span>.0</span>
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<pre style="margin: 0;">+<span id="LC13" 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="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/uc-echo</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/uc-echo.git</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: http://uc-echo.sourceforge.net/</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">@@ -20,11 +19,11 @@ Package: uc-echo</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> python-scipy</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ${python<span class="idiff left right">3</span>:Depends},</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-scipy</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: error correction algorithm designed for short-reads from NGS</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> ECHO is an error correction algorithm designed for short-reads<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> from next-generation sequencing platforms such as Illumina's<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> Genome Analyzer II. The algorithm uses a Bayesian framework to<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> improve the quality of the reads in a given data set by employing<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> ECHO is an error correction algorithm designed for short-reads</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> from next-generation sequencing platforms such as Illumina's</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> Genome Analyzer II. The algorithm uses a Bayesian framework to</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> improve the quality of the reads in a given data set by employing</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> maximum a posteriori estimation.</span></pre>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/uc-echo/compare/1271416909837719c8dcc1204aa489ebebabc251...58584eacc2504c7657a3d1a4ea3a4c152ffe27d0#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/938741</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: Mon, 02 Sep 2019 21:21:16 +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/ErrorCorrection.py</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/ErrorCorrection.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1,3 +1,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" 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="LC10" 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="LC11" class="line" lang="diff"> import subprocess</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> import threading</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> import itertools</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -82,7 +84,7 @@</span> class LogMgr:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> self.logfile.write("%s\n"%output_str)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> self.logfile.flush()</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if Verbose or console_output:</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;">- print output_str + "\n"</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;">+ print(output_str + "\n")</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"> ##########################</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -110,7 +112,7 @@</span> class CmdExecuter:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> proc = subprocess.Popen(cmd, bufsize=10240, stdout=subprocess.PIPE, stderr=subprocess.PIPE)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> stdout, stderr = proc.communicate()</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> if stdout != "":</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print stdout</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;">+ print(stdout)</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> returncode = proc.returncode</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> if stderr is not None and len(stderr)>0:</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> MsgLogger.log("ERROR: " + stderr, True)</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -174,7 +176,7 @@</span> def poiTotalVar(hist):</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> poi_pmf = poisson.pmf(arange(len(hist)), m)</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> residual_mass = 1.0 - sum(poi_pmf)</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- total_var = 0.5*sum( abs(p1-p2) for p1, p2 in itertools.izip(emp_pmf, poi_pmf)) + 0.5*residual_mass</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ total_var = 0.5*sum( abs(p1-p2) for p1, p2 in zip(emp_pmf, poi_pmf)) + 0.5*residual_mass</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> if total_var < est_tv:</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> est_tv = total_var</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="p">@@ -302,7 +304,7 @@</span> def Hashing(cmdexecuter, target_st, targ</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> HashFiles[0].append(os.path.join(TmpDIR, "%d.hash"%(read_st)))</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> IndexFiles[0].append(os.path.join(TmpDIR, "%d.index"%(read_st)))</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> assert(len(HashFiles) == len(IndexFiles))</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(len(HashFiles)):</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(len(HashFiles)):</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> assert(len(HashFiles[i]) == len(IndexFiles[i]))</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> if len(HashFiles[i])>=ReadMergeBatchSize or (len(HashFiles[i])>=1 and cur_hash_file==tot_num_hash_files-1):</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> #cmdexecuter.wait()</span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="p">@@ -311,7 +313,7 @@</span> def Hashing(cmdexecuter, target_st, targ</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> IndexFiles.append([])</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> # Run appropriate merging</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> if len(HashFiles[i]) > 1:</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- inputFNames = list(itertools.chain(*zip(HashFiles[i], IndexFiles[i])))</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ inputFNames = list(itertools.chain(*list(zip(HashFiles[i], IndexFiles[i]))))</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> cmdexecuter.exeCmd(makeHashMergeCmd(inputFNames, TmpDIR, "t_%d_%d"%(i+1, len(HashFiles[i+1]))))</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> cmdexecuter.wait()</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> elif len(HashFiles[i]) == 1:</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -339,10 +341,10 @@</span> def Hashing(cmdexecuter, target_st, targ</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> def Neighboring(cmdexecuter, target_st, target_ed, DataBlockSize, nData, paramK, paramh, parame, maxCov, NHashFile, nKmers, param):</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> # DataBlockSize should be nData (the entire data set)</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> CachedBlocks = set()</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for read_st in xrange(target_st, target_ed, DataBlockSize):</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for read_st in range(target_st, target_ed, DataBlockSize):</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> #read_ed = min(read_st + DataBlockSize, nData)</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> read_ed = min(target_ed, nData)</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for read_st2 in xrange(0, nData, DataBlockSize):</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for read_st2 in range(0, nData, DataBlockSize):</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> read_ed2 = min(read_st2 + DataBlockSize, nData)</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> if read_st<=read_st2:</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -357,7 +359,7 @@</span> def Neighboring(cmdexecuter, target_st,</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> # Create empty neighbor file</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> NeighborFiles = [[]]</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for hashfile in xrange(NHashFile):</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for hashfile in range(NHashFile):</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> # NeighborJoin for each hash block</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> ihash_st = hashfile*nKmers/NHashFile</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> ihash_ed = (hashfile+1)*nKmers/NHashFile</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="p">@@ -373,7 +375,7 @@</span> def Neighboring(cmdexecuter, target_st,</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> # NeighborMerge</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> # Merge together adjacency lists into one main adjacency list</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> NeighborFiles[0].append(os.path.join(TmpDIR, "neighbors_%d_%d_%d.list"%(hashfile, st, st2)))</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(len(NeighborFiles)):</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(len(NeighborFiles)):</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> if len(NeighborFiles[i])>=HashMergeBatchSize or (len(NeighborFiles[i])>=1 and hashfile==NHashFile-1):</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> # Extend list if another level of "tree" is added</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> if len(NeighborFiles)==i+1:</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="p">@@ -461,7 +463,7 @@</span> if __name__ == '__main__':</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> # Check for existence of input file</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> if not os.path.isfile(OrigReadFName):</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR: Input file " + OrigReadFName + " does not exist."</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR: Input file " + OrigReadFName + " does not exist.")</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> sys.exit(1)</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> # Create log directory</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="p">@@ -619,10 +621,10 @@</span> if __name__ == '__main__':</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> fin = file_open_function(OrigReadFName, "r")</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> try:</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> while True:</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- line0 = fin.next()</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- line1 = fin.next()</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- line2 = fin.next()</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- line3 = fin.next()</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ line0 = next(fin)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ line1 = next(fin)</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;">+ line2 = next(fin)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ line3 = next(fin)</span></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"> # Quick sanity checks to ensure FASTQ format</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> assert(line0[0] == "@")</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="p">@@ -668,7 +670,7 @@</span> if __name__ == '__main__':</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> ModelSelectionSetSize = min(options.msize, nData)</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> random.seed(1)</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SeqOrdering = range(nData)</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SeqOrdering = list(range(nData))</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> random.shuffle(SeqOrdering)</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> with open(TmpFile.name, "r") as fin:</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="p">@@ -677,7 +679,7 @@</span> if __name__ == '__main__':</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> for idx in SeqOrdering:</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> fout.write(struct.pack("Q", ReadSt[idx]))</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>
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<td class="diff-line-num new new_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line, id in itertools.izip(fin, itertools.count()):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line, id in zip(fin, itertools.count()):</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> line = line.strip()</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> if id%2==0:</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> fout.write("Y%s\x00"%line)</span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="p">@@ -740,7 +742,7 @@</span> if __name__ == '__main__':</span>
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<td class="diff-line-num new new_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> nKmers = int(struct.unpack("@I", tmpfile.read(4))[0])</span>
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<td class="diff-line-num new new_line" data-linenumber="134" 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">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> if nKmers < 0:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "ERROR: Number of kmers in " + os.path.join(TmpDIR, "all.index") + " is not valid."</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("ERROR: Number of kmers in " + os.path.join(TmpDIR, "all.index") + " is not valid.")</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> sys.exit(1)</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>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="p">@@ -886,7 +888,7 @@</span> if __name__ == '__main__':</span>
</pre>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> for read_st in range(0, nData, nData):</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> with open(os.path.join(TmpDIR, "output_%d_%d_%f.txt"%(read_st, best_paramh, best_parame)), "r") as fin:</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> with open(os.path.join(TmpDIR, "quality_%d_%d_%f.txt"%(read_st, best_paramh, best_parame)), "r") as qualfin:</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line, qualline in itertools.izip(fin,qualfin):</span></span>
</pre>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line, qualline in zip(fin,qualfin):</span></span>
</pre>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> readmap[ReadSt[SeqOrdering[cur_read_order]]:(ReadSt[SeqOrdering[cur_read_order]]+ReadLen[SeqOrdering[cur_read_order]]+1)] = line.strip() + '\n'</span>
</pre>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> qualmap[ReadSt[SeqOrdering[cur_read_order]]:(ReadSt[SeqOrdering[cur_read_order]]+ReadLen[SeqOrdering[cur_read_order]]+1)] = qualline.strip() + '\n'</span>
</pre>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> cur_read_order += 1</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="p">@@ -898,14 +900,14 @@</span> if __name__ == '__main__':</span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> # Eliminate reverse complement reads</span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> with open(OutputFName+".seq", "w+b") as fout:</span>
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<td class="diff-line-num new new_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> with open(TmpFile.name, "r") as fin:</span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (line, counter) in itertools.izip(fin, itertools.count()):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="155" 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">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (line, counter) in zip(fin, itertools.count()):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> if counter%2==0:</span>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> fout.write(line)</span>
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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="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> os.unlink(TmpFile.name)</span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> with open(OutputFName+".qual", "w+b") as fout:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> with open(QualTmpFile.name, "r") as fin:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (line, counter) in itertools.izip(fin, itertools.count()):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (line, counter) in zip(fin, itertools.count()):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> if counter%2==0:</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="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> fout.write(line)</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="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> os.unlink(QualTmpFile.name)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="p">@@ -913,7 +915,7 @@</span> if __name__ == '__main__':</span>
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<td class="diff-line-num new new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> with open(OutputFName, "w+b") as fout:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="169" 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">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> with open(OutputFName+".seq", "r") as fseq:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="170" 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">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> with open(OutputFName+".qual", "r") as fqual:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (seq, qual, id) in itertools.izip(fseq, fqual, itertools.count()):</span></span>
</pre>
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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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (seq, qual, id) in zip(fseq, fqual, itertools.count()):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> fout.write("@%d\n%s\n+\n%s\n"%(id, seq.strip(), qual.strip()))</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> if not KeepAllFiles:</span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/README</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span> Quickstart:</span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> > make</span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> 2. In the same directory, type:</span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- > python ErrorCorrection.py -o output/sample_data.fastq sample_data.txt</span></span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ > ErrorCorrection.py -o output/sample_data.fastq sample_data.txt</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> - sample_data.txt is the input file.</span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> - output/sample_data.fastq is the output file name.</span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="p">@@ -43,7 +43,7 @@</span> Quickstart:</span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> 4. The output file sample_data.fastq.seq can be compared to sample_answer.txt, which contains the original reads without errors. There will be differences between sample_data.fastq.seq and sample_answer.txt because not every error is corrected by the error correction.</span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> 5. To run with 4 threads, type</span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- > python ErrorCorrection.py --ncpu 4 -o output/sample_data.fastq sample_data.txt</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ > ErrorCorrection.py --ncpu 4 -o output/sample_data.fastq sample_data.txt</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> Installation:</span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> ------------</span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="p">@@ -74,12 +74,12 @@</span> Note that the parsing method used by ECH</span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> The output file format of ECHO is standard FASTQ format.</span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> To run ECHO, use the following command</span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-> python ErrorCorrection.py -o output.fastq input.txt</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+> ErrorCorrection.py -o output.fastq input.txt</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> NOTE: The above command will generally work on relatively small data set sizes. The exact size depends on the amount of avaiable RAM. Please read the below 'Notes on Memory Usage' for additional details on running ECHO on larger data sets.</span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> Help messages for additional options can be found by using</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-> python ErrorCorrection.py -h</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+> ErrorCorrection.py -h</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> Notes on Memory Usage:</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> ---------------------</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="p">@@ -96,10 +96,10 @@</span> These parameters are set on the command</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> Examples:</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> For 5M reads, the following will typically run well with 8GB memory:</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-> python ErrorCorrection.py -b 2000000 --nh 256 -o output/5Mreads.fastq 5Mreads.txt</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+> ErrorCorrection.py -b 2000000 --nh 256 -o output/5Mreads.fastq 5Mreads.txt</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> For 20M reads, the following will typically run well with 8GB memory:</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-> python ErrorCorrection.py -b 2000000 --nh 1024 -o output/20Mreads.fastq 20Mreads.txt</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+> ErrorCorrection.py -b 2000000 --nh 1024 -o output/20Mreads.fastq 20Mreads.txt</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> Using Multiple Threads: </span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> ----------------------</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="p">@@ -107,7 +107,7 @@</span> Use the --ncpu command line option to se</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> Example:</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> To use 6 threads at once:</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-> python ErrorCorrection.py -b 2000000 --nh 256 --ncpu 6 -o output/5Mreads.fastq 5Mreads.txt</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+> ErrorCorrection.py -b 2000000 --nh 256 --ncpu 6 -o output/5Mreads.fastq 5Mreads.txt</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> </span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> Log files:</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> ---------</span></pre>
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<a href="https://salsa.debian.org/med-team/uc-echo/compare/1271416909837719c8dcc1204aa489ebebabc251...58584eacc2504c7657a3d1a4ea3a4c152ffe27d0#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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="plaintext">hardening-flags.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">include.patch</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">m64-flag.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/uc-echo/compare/1271416909837719c8dcc1204aa489ebebabc251...58584eacc2504c7657a3d1a4ea3a4c152ffe27d0#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">@@ -9,7 +9,7 @@ CPATH=/usr/include/$(DEB_HOST_MULTIARCH)</td>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export LIBRARY_PATH CPATH</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">ADDCXXFLAGS = -m64</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">ifeq ($(DEB_HOST_ARCH),$(filter $(DEB_HOST_ARCH),mips mipsel mipsn32 mipsn32el mips64 mips64el hppa kfreebsd-i386 hurd-i386 armel armhf arm64 ia64 sh4 powerpcspe m68k))</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">ADDCXXFLAGS =<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">ADDCXXFLAGS =</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">CXXFLAGS += $(ADDCXXFLAGS)</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">@@ -17,7 +17,7 @@ CXXFLAGS += $(ADDCXXFLAGS)</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">3</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> echo "I: DEB_HOST_ARCH: $(DEB_HOST_ARCH)"</span>
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<li id="47a651b586e42387ccdfca5a878d963be2a87da5">
<a href="https://salsa.debian.org/med-team/uc-echo/compare/1271416909837719c8dcc1204aa489ebebabc251...58584eacc2504c7657a3d1a4ea3a4c152ffe27d0#47a651b586e42387ccdfca5a878d963be2a87da5"><strong>debian/script/uc-echo</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="idiff left right">python </span>/usr/lib/uc-echo/ErrorCorrection.py <span class="nv" style="color: #008080;">$@</span></span></pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell">/usr/lib/uc-echo/ErrorCorrection.py <span class="nv" style="color: #008080;">$@</span></span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/uc-echo/compare/1271416909837719c8dcc1204aa489ebebabc251...58584eacc2504c7657a3d1a4ea3a4c152ffe27d0#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</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="plaintext">version=3</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">opts="uversionmangle=s/_/./" \</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> http://sf.net/uc-echo/echo_v([\d_]+)\.tgz</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> http<span class="idiff left right">s</span>://sf.net/uc-echo/echo_v([\d_]+)\.tgz</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span></pre>
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