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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/wtdbg2">Debian Med / wtdbg2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/13211a71559440f107d7690777003cd2d680ebcf">13211a71</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-09T14:49:01+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/8d220b6f177be6cec77d4ea23ed241064aeef347">8d220b6f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-09T14:49:22+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Save up space by not extracting the binary
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/89f01792ecdef50c4be8133f042097ad54badbb2">89f01792</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-09T14:49:45+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New binary: wtdbg2-examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/13b8ea5bf393386a3eec95defc565d79b37a1e6c">13b8ea5b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-09T14:50:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor fixes on manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/7b2d763bec06fe3a2a8b91171fc14b0cc89d3211">7b2d763b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-09T20:28:05+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spellings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/e56ba7735427e54e99ee73d083a4ee8a78724aa2">e56ba773</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-09T20:34:28+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Change arch of example binary to all
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#c53602ea1ca3d255ecfb64bfe9eae44011e49ce8">
debian/mans/kbm2.1
</a>
</li>
<li class="file-stats">
<a href="#acc739822f4ab41c75e37b0dd9537acc5279a54e">
debian/mans/wtdbg2.1
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
<span class="new-file">
+
debian/source/include-binaries
</span>
</a>
</li>
<li class="file-stats">
<a href="#14fea0078728545f6a156de7c63df9f8ed927ef8">
<span class="new-file">
+
debian/tests/README
</span>
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#5ae2d2e4f579b7473ab916ae821c0858aea8428e">
<span class="new-file">
+
debian/tests/data/selfSampleData.tar.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
<li class="file-stats">
<a href="#48d8833cec087c470c36dd8b43669caee2416778">
<span class="new-file">
+
debian/wtdbg2-examples.docs
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
<hr>
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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">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="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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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> zlib1g-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libsimde-dev</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="9" 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">
9
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<td class="diff-line-num new_line" data-linenumber="9" 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">
9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="19" 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">@@ -19,7 +19,8 @@ Depends: ${shlibs:Depends},</td>
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<td class="diff-line-num old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext">Suggests: ${perl:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> minimap2,</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> samtools,</span>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC22" class="line" lang="plaintext"> mummer</span>
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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> mummer,</span>
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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Recommends: wtdbg2-examples</span>
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<td class="diff-line-num old_line" data-linenumber="23" 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">
23
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<td class="diff-line-num new_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext">Description: de novo sequence assembler for long noisy reads</span>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="25" 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="LC25" class="line" lang="plaintext"> Wtdbg2 is a de novo sequence assembler for long noisy reads produced by</span>
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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" class="line" lang="plaintext"> PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads</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">@@ -34,3 +35,19 @@ Description: de novo sequence assembler for long noisy reads</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> (FBG). It is akin to De Bruijn graph but permits mismatches/gaps and</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> keeps read paths when collapsing k-mers. The use of FBG distinguishes</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> wtdbg2 from the majority of long-read assemblers.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Package: wtdbg2-examples</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Enhances: wtdbg2</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Description: Examples for wtdbg - de novo sequence assembler</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> Wtdbg2 is a de novo sequence assembler for long noisy reads produced by</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> without error correction and then builds the consensus from intermediate</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> assembly output. Wtdbg2 is able to assemble the human and even the 32Gb</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> Axolotl genome at a speed tens of times faster than CANU and FALCON</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> while producing contigs of comparable base accuracy.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> This package contains a test data set as well as sample scripts</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> running some test suite provided by Debian also as autopkgtest.</span></pre>
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<li id="c53602ea1ca3d255ecfb64bfe9eae44011e49ce8">
<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2#c53602ea1ca3d255ecfb64bfe9eae44011e49ce8"><strong>debian/mans/kbm2.1</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">@@ -56,7 +56,7 @@ Filter low complexity bins (#indexed_kmer less than <\-O>), [2]</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">\fB\-S\fR <float></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">Subsampling kmers, 1/(<\-S>) kmers are indexed, [4.00]</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">\fB\-S\fR is very useful in saving mem<span class="idiff left right">e</span>ory and speeding up</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">\fB\-S\fR is very useful in saving memory and speeding up</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">please note that subsampling kmers will have less matched length</span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">.TP</span>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">\fB\-B\fR <int></span>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2#acc739822f4ab41c75e37b0dd9537acc5279a54e"><strong>debian/mans/wtdbg2.1</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">@@ -58,7 +58,7 @@ Filter high frequency kmers, maybe repetitive, [1000.05]</td>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">.TP</span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">\fB\-S\fR <float></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">Subsampling kmers, 1/(<\-S>) kmers are indexed, [4.00]</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">\fB\-S\fR is very useful in saving mem<span class="idiff left right">e</span>ory and speeding up</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">\fB\-S\fR is very useful in saving memory and speeding up</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">please note that subsampling kmers will have less matched length</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">\fB\-l\fR <float></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" 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">@@ -178,7 +178,7 @@ Retain dovetail overlaps only, the max overhang size is <\-\-aln\-dovetail>, the</td>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext">.HP</span>
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext">\fB\-\-aln\-strand\fR <int></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="plaintext">.IP</span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext">1: forward, 2: reverse, 3: both. Please don't change the deault va<span class="idiff left right">ul</span>e 3, unless you exactly know what you are doing</span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">1: forward, 2: reverse, 3: both. Please don't change the deault va<span class="idiff left right">lu</span>e 3, unless you exactly know what you are doing</span>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext">\fB\-\-aln\-maxhit\fR <int></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="plaintext">.IP</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">@@ -303,7 +303,7 @@ Don't attempt to rescue low coverage edges</td>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="plaintext">\fB\-\-node\-min\fR <int></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="plaintext">.IP</span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="plaintext">Min depth of an interval to be selected as valid node. Defaultly, this value is automaticly the same with \fB\-\-edge\-min\fR.</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">Min depth of an interval to be selected as valid node. Defaultly, this value is automatic<span class="idiff left right">al</span>ly the same with \fB\-\-edge\-min\fR.</span>
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307
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="plaintext">.HP</span>
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308
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="plaintext">\fB\-\-node\-max\fR <int></span>
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309
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="364" 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">@@ -364,7 +364,7 @@ Min length of contigs to be output, 5000</td>
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364
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="plaintext">.HP</span>
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365
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="plaintext">\fB\-\-ctg\-min\-nodes\fR <int></span>
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366
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="plaintext">.IP</span>
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367
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="plaintext">Min num of nodes in a contig to be ouput, 3</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">Min num of nodes in a contig to be ou<span class="idiff left right">t</span>put, 3</span>
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368
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="plaintext">.HP</span>
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369
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="plaintext">\fB\-\-minimal\-output\fR</span>
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370
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="plaintext">.IP</span>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2#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">@@ -19,6 +19,12 @@ libexecdir=$(prefix)/lib/$(DEB_SOURCE)</td>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> dh $@</span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> sed -i 's/\/usr\/bin\/env perl/\/usr\/bin\/perl/' scripts/*</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> sed -i 's/memeory/memory/' *.c *.h *.md</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> sed -i 's/automaticly/automatically/' *.c</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> sed -i 's/ouput/output/' *.c</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> sed -i 's/vaule/value/' *.c</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> sed -i 's/annonymous/anonymous/' *.h</span>
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22
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> mkdir -p $(prefix)</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> mkdir -p $(libexecdir)</span>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/data/selfSampleData.tar.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2#14fea0078728545f6a156de7c63df9f8ed927ef8"><strong>debian/tests/README</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests for wtdbg2</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">=================</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">The data for tests has been referenced from:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, bwa, minimap2, samtools</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2#5ae2d2e4f579b7473ab916ae821c0858aea8428e"><strong>debian/tests/data/selfSampleData.tar.gz</strong></a>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/7fe1a0d7eef40d354a8bba4b56a1fd2149cbbf63...e56ba7735427e54e99ee73d083a4ee8a78724aa2#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>wtdbg2</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-examples</span>/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xvf</span> <span class="k" style="font-weight: 600;">*</span>.tar</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>selfSampleData</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Checks whether file checksum is same as expected</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>check_same<span class="o" style="font-weight: 600;">()</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># $1 : file name</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># $2 : checksum value</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$1</span> | <span class="nb" style="color: #0086b3;">md5sum</span> | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'{print $1}'</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="nv" style="color: #008080;">$2</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Begin Execution"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">wtdbg2 <span class="nt" style="color: #000080;">-t</span> 16 <span class="nt" style="color: #000080;">-x</span> rs <span class="nt" style="color: #000080;">-g</span> 4.6m <span class="nt" style="color: #000080;">-o</span> dbg pacbio_filtered.fastq</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Step by step commandlines</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># assemble long reads</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">wtdbg2 <span class="nt" style="color: #000080;">-x</span> rs <span class="nt" style="color: #000080;">-g</span> 4.6m <span class="nt" style="color: #000080;">-i</span> pacbio_filtered.fastq <span class="nt" style="color: #000080;">-t</span> 16 <span class="nt" style="color: #000080;">-fo</span> dbg</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># derive consensus</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">wtpoa-cns <span class="nt" style="color: #000080;">-t</span> 16 <span class="nt" style="color: #000080;">-i</span> dbg.ctg.lay.gz <span class="nt" style="color: #000080;">-fo</span> dbg.raw.fa</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell">check_same dbg.raw.fa a2c479242d7c6ad6c8ffd979b821aa01</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># polish consensus, not necessary if you want to polish the assemblies using other tools</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell">minimap2 <span class="nt" style="color: #000080;">-t16</span> <span class="nt" style="color: #000080;">-ax</span> map-pb <span class="nt" style="color: #000080;">-r2k</span> dbg.raw.fa pacbio_filtered.fastq | samtools <span class="nb" style="color: #0086b3;">sort</span> -@4 <span class="o" style="font-weight: 600;">></span>dbg.bam</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">samtools view <span class="nt" style="color: #000080;">-F0x900</span> dbg.bam | wtpoa-cns <span class="nt" style="color: #000080;">-t</span> 16 <span class="nt" style="color: #000080;">-d</span> dbg.raw.fa <span class="nt" style="color: #000080;">-i</span> - <span class="nt" style="color: #000080;">-fo</span> dbg.cns.fa</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell">check_same dbg.cns.fa 62a41e5cb7a5e702523237f4ab65c376</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"></span></pre>
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