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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/dextractor">Debian Med / dextractor</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/dextractor/-/commit/6628e5433435f2b5b2f59fc90d67bee5394da331">6628e543</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-06-29T17:32:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix lintian error for control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dextractor/-/commit/2539a0727db6afa5326a0be118728951276bc76c">2539a072</a></strong>
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<span>by Shayan Doust</span>
<i>at 2020-06-29T17:43:20+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More new manpages
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#ab8a81dcb05d733c5fe5a4966decb34d4282de30">
debian/mans/dexta.1
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<li class="file-stats">
<a href="#621c323fb70b0386f44d9e2852b20e40681a2d06">
<span class="new-file">
+
debian/mans/undexqv.1
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<li class="file-stats">
<a href="#bda40b4f418f8afc52154f6db26896c949a55a12">
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+
debian/mans/undexta.1
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/dextractor/-/compare/07a3603c909917dd862c5a1aaffd82e432effa8b...2539a0727db6afa5326a0be118728951276bc76c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" 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">@@ -14,14 +14,14 @@ Package: dextractor</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Description: <span class="idiff left right">the D</span>extractor and compression command library</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext"> <span class="idiff left right">The </span>Dextractor commands allow one to pull exactly and only the</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Description: <span class="idiff left right">(d)</span>extractor and compression command library</span>
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<td class="diff-line-num new old_line" data-linenumber="19" 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="18" 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="LC18" class="line" lang="plaintext"> Dextractor commands allow one to pull exactly and only the</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> information needed for assembly and reconstruction from the source HDF5</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> files produced by the PacBio RS II sequencer, or from the source BAM</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> files produced by the PacBio Sequel sequencer.</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"> For each of the three extracted file types -- <span class="idiff left right">.fasta, .</span>quiva, and </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> <span class="idiff left right">.</span>arrow -- the library contains commands to compress the given file</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> For each of the three extracted file types -- <span class="idiff left right">fasta, </span>quiva, and </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> arrow -- the library contains commands to compress the given file</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> type, and to decompress it, which is a reversible process delivering</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> the original uncompressed file. The compressed .fasta files, with the</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> extension .dexta, consume 1/4 byte per base. The compressed .quiva</span>
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<li id="ab8a81dcb05d733c5fe5a4966decb34d4282de30">
<a href="https://salsa.debian.org/med-team/dextractor/-/compare/07a3603c909917dd862c5a1aaffd82e432effa8b...2539a0727db6afa5326a0be118728951276bc76c#ab8a81dcb05d733c5fe5a4966decb34d4282de30"><strong>debian/mans/dexta.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">@@ -12,7 +12,7 @@ With the -k option the .fasta source is not removed. If -v is set, then the prog</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">With the -i option set, the program runs as a UNIX pipe that takes .fasta (.dexta) input from the standard input and writes .dexta (.fasta) to the standard output. In this case the -k option has no effect.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">The full documentation for</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.B dexta<span class="idiff left right">:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.B dexta</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">is maintained as a Texinfo manual. If the</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">.B info</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">and</span>
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<a href="https://salsa.debian.org/med-team/dextractor/-/compare/07a3603c909917dd862c5a1aaffd82e432effa8b...2539a0727db6afa5326a0be118728951276bc76c#621c323fb70b0386f44d9e2852b20e40681a2d06"><strong>debian/mans/undexqv.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH UNDEXQV "1" "June 2020" "undexqv" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">undexqv \- uncompress a set of .dexqv files</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.B undexqv</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">[\fI\,-vkl\/\fR] \fI\,<path:dexqv> \/\fR...</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Undexqv takes a set of .dexqv files as input and decompresses it. The result is that it will generate new uncompressed .quiva files.</span>
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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">Please refer to</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.B man dexqv </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">for a description of the *dexqv commands and their uses.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">The full documentation for</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.B undexqv</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">is maintained as a Texinfo manual. If the</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.B info</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">and</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.B undexqv</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">programs are properly installed at your site, the command</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.B info undexqv</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">should give you access to the complete manual.</span></pre>
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<a href="https://salsa.debian.org/med-team/dextractor/-/compare/07a3603c909917dd862c5a1aaffd82e432effa8b...2539a0727db6afa5326a0be118728951276bc76c#bda40b4f418f8afc52154f6db26896c949a55a12"><strong>debian/mans/undexta.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH UNDEXTA "1" "June 2020" "undexta" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">undexta \- uncompress a set of .dexta files</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.B undexta</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">[\fI\,-vk\/\fR] \fI\,<path:dexta> \/\fR...</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Undexta takes in a set of .dexta files as input, and uncompresses it. The result uncompressed .fasta files.</span>
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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">Please refer to</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.B man dexta </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">for the full operation of the *dexta commands and its uses.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.SH "SEE ALSO"</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">The full documentation for</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.B undexta</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">is maintained as a Texinfo manual. If the</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.B info</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">and</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.B undexta</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">programs are properly installed at your site, the command</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.B info undexta</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">should give you access to the complete manual.</span></pre>
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