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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqmagick">Debian Med / seqmagick</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/commit/a50ad8d6fb633537472228c8f0d8c184955d83ec">a50ad8d6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-14T21:11:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial packaging, some test suite errors are remainig
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqmagick/commit/06dc2157fd006b25d11866542f03012368df3b16">06dc2157</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-14T21:49:25+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Test suite has issues - reported upstream
</pre>
</li>
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<h4>10 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
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+
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
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+
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
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debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
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debian/copyright
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<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
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debian/createmanpages
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<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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debian/manpages
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debian/rules
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<a href="#eebd58f645086af566297cb3d59c9fa7b409ce14">
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debian/seqmagick.1
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debian/source/format
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debian/watch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">seqmagick (0.7.0-1) UNRELEASED; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</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"> TODO: https://github.com/fhcrc/seqmagick/issues/73</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></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"> -- Andreas Tille <tille@debian.org> Thu, 22 Jun 2017 12:03:20 +0200</span></pre>
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</li>
<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</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">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: seqmagick</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh-python,</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"> python3-all,</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"> python3-setuptools,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-nose,</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3-biopython</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.1.4</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">Vcs-Browser: https://salsa.debian.org/med-team/seqmagick</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/seqmagick.git</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Homepage: https://github.com/fhcrc/seqmagick/</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Package: seqmagick</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python3-biopython</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Description: imagemagick-like frontend to Biopython SeqIO</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> Seqmagick is a little utility to expose the file format conversion</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> in BioPython in a convenient way.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> Features include:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> * Modifying sequences:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> - Remove gaps</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> - Reverse & reverse complement</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> - Trim to a range of residues</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> - Change case</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> - Sort by length or ID</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> * Displaying information about sequence files</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> * Subsetting sequence files by:</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> - Position</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> - ID</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> - Deduplication</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> * Filtering sequences by quality score</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> * Trimming alignments to a region of interest defined by the forward</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> and reverse primers</span></pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Source: https://github.com/fhcrc/seqmagick/releases</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Files: *</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Copyright: 2014-2017 Matsen Group</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">License: GPL-3+</span>
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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: debian/*</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Copyright: 2017 Andreas Tille <tille@debian.org></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">License: GPL-3+</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">License: GPL-3+</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> This program is free software: you can redistribute it and/or modify</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> the Free Software Foundation, either version 3 of the License, or</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> (at your option) any later version.</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> This program is distributed in the hope that it will be useful,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> On Debian systems you can find a copy of the full text of the GNU General</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> Public License version 3 at /usr/share/common-licenses/GPL-3.</span></pre>
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<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</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/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: teal;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell">mkdir <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$MANDIR</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | awk <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | sed <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: teal;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: teal;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>seqmagick</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'Manipulate sequence files'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$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;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$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="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" 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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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="no" style="color: teal;">EOT</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</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"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span></pre>
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<a href="https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16#eebd58f645086af566297cb3d59c9fa7b409ce14"><strong>debian/seqmagick.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SEQMAGICK "1" "June 2017" "seqmagick 0.6.1" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">seqmagick \- Manipulate sequence files</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">usage: seqmagick [\-h] [\-V] [\-v] [\-q]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">{help,convert,info,mogrify,primer\-trim,quality\-filter,extract\-ids,backtrans\-align}</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">\&...</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH DESCIPTION</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Seqmagick is a little utility to expose the file format conversion</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">in BioPython in a convenient way.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.SH OPTIONS</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.SS "positional arguments:"</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.IP</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">{help,convert,info,mogrify,primer\-trim,quality\-filter,extract\-ids,backtrans\-align}</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">help</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Detailed help for actions using help <action></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">convert</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Convert between sequence formats</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">info</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Info action</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">mogrify</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Modify sequence file(s) in place.</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">primer\-trim</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Find a primer sequence in a gapped alignment, trim to</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">amplicon</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">quality\-filter</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Filter reads based on quality scores</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.TP</span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">extract\-ids</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Extract the sequence IDs from a file</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">backtrans\-align</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Given a protein alignment and unaligned nucleotides,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="42" 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">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">align the nucleotides using the protein alignment.</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Protein and nucleotide sequence files must contain the</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">same number of sequences, in the same order, with the</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">same IDs.</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.SS "optional arguments:"</span>
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<td class="diff-line-num new new_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">show this help message and exit</span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.TP</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">\fB\-V\fR, \fB\-\-version\fR</span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Print the version number and exit</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.TP</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">\fB\-v\fR, \fB\-\-verbose\fR</span>
</pre>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Be more verbose. Specify \fB\-vv\fR or \fB\-vvv\fR for even more</span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.TP</span>
</pre>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">\fB\-q\fR, \fB\-\-quiet\fR</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">Suppress output</span>
</pre>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.SH AUTHOR</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="53399f7f2dd7535c43cdcfa511a9c06044a9c238">
<a href="https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/seqmagick/compare/44293af7d8be49dfc985f88f1c5f779a51df68ba...06dc2157fd006b25d11866542f03012368df3b16#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">https://github.com/fhcrc/seqmagick/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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