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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pilon-non-free">Debian Med / pilon-non-free</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pilon-non-free/commit/9f715bf8325116fa1ca4056dbcdadca5e71d6b9b">9f715bf8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-12T14:43:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pilon-non-free/commit/52c96edc7a9fea60fe7fa78065b71924206ebcda">52c96edc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-16T16:26:40+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Document bug that is responsible why we can not build pilon
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/pilon-non-free/commit/97d870df6484d8e2ad8755c720bcc6e852428de0">97d870df</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-16T16:46:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to new
</pre>
</li>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
debian/createmanpages
</a>
</li>
<li class="file-stats">
<a href="#1cb7bbaf0bb6ea80762a8dacf7cb8d437cf65eac">
debian/pilon.1
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pilon-non-free/compare/664bae39d91bf2c6380218b899559c33ba743ac5...97d870df6484d8e2ad8755c720bcc6e852428de0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">pilon-non-free (1.22-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pilon-non-free (1.22-1) <span class="idiff left right">unstable</span>; urgency=medium</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"> * Initial release (Closes: #<span class="idiff left right"><bug></span>)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">903911</span>)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Thu, 23 Feb 2017 16:48:18 +01</span>00</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Mon, 16 Jul 2018 16:46:04 +02</span>00</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/pilon-non-free/compare/664bae39d91bf2c6380218b899559c33ba743ac5...97d870df6484d8e2ad8755c720bcc6e852428de0#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">5</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pilon-non-free</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pilon-non-free.git</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Homepage: https://github.com/broadinstitute/pilon/wiki</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,5 +36,5 @@ Description: automated genome assembly improvement and variant detection tool</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> The code of pilon is actually free but currently there is no method</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> to build the JAR from the scala source in Debian. This package is</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> supposed to be replaced by a pilon package once it can be build from</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> source.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> source<span class="idiff left right"> (see bug #873341)</span>.</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/pilon-non-free/compare/664bae39d91bf2c6380218b899559c33ba743ac5...97d870df6484d8e2ad8755c720bcc6e852428de0#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ Upstream-Name: pilon</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: https://github.com/broadinstitute/pilon/issues</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: https://github.com/broadinstitute/pilon/releases</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Comment: The code is actually free but currently there is no method</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> to build</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> to build<span class="idiff left right"> (see bug #873341)</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Copyright: Copyright 2012-2017 Broad Institute, Inc.</span>
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<a href="https://salsa.debian.org/med-team/pilon-non-free/compare/664bae39d91bf2c6380218b899559c33ba743ac5...97d870df6484d8e2ad8755c720bcc6e852428de0#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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">@@ -18,7 +18,10 @@ help2man --no-info --no-discard-stderr --help-option=" --help" \</td>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="s1" style="color: #d14;">'s/specifed/specified/'</span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/specifed/specified/'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/minumum/minimum/'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOT</span></span>
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24
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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<a href="https://salsa.debian.org/med-team/pilon-non-free/compare/664bae39d91bf2c6380218b899559c33ba743ac5...97d870df6484d8e2ad8755c720bcc6e852428de0#1cb7bbaf0bb6ea80762a8dacf7cb8d437cf65eac"><strong>debian/pilon.1</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" 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="187" 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">@@ -187,7 +187,7 @@ Kmer size used by internal assembler (default 47).</td>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="plaintext">Variants (snps and indels) will only be called if there is coverage of good pairs</span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="plaintext">at this depth or more; if this value is >= 1, it is an absolute depth, if it is a</span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="plaintext">fraction < 1, then minimum depth is computed by multiplying this value by the mean</span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext">coverage for the region, with a min<span class="idiff left right">u</span>mum value of 5 (default 0.1: min depth to call</span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">coverage for the region, with a min<span class="idiff left right">i</span>mum value of 5 (default 0.1: min depth to call</span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="plaintext">is 10% of mean coverage or 5, whichever is greater).</span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="plaintext">\fB\-\-mingap\fR</span>
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