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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bismark">Debian Med / bismark</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/bismark/-/commit/4601499e4a3ba29e51e6109aae708ac76fe1e70f">4601499e</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-21T11:38:01+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Provide description
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<h4>1 changed file:</h4>
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bismark/-/commit/4601499e4a3ba29e51e6109aae708ac76fe1e70f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: bismark</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Priority: optional</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: Liubov Chuprikova <chuprikovalv@gmail.com></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 (>= 12~)</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3</span>.0</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5</span>.0</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bismark</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bismark.git</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Homepage: https://www.bioinformatics.babraham.ac.uk/projects/bismark/</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Package: bismark</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends},</span>
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<td class="diff-line-num old old_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> perl,</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ${perl:Depends},</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> bowtie2,</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> hisat2</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Description: A bisulfite read mapper and methylation caller</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> <long_description></span></pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> hisat2</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Description: bisulfite read mapper and methylation caller</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Bismark is a program to map bisulfite treated sequencing reads to a</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> genome of interest and perform methylation calls in a single step. The</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> output can be easily imported into a genome viewer, such as SeqMonk, and</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> enables a researcher to analyse the methylation levels of their samples</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> straight away. It's main features are:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> * Bisulfite mapping and methylation calling in one single step</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> * Supports single-end and paired-end read alignments</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> * Supports ungapped and gapped alignments</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> * Alignment seed length, number of mismatches etc. are adjustable</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> * Output discriminates between cytosine methylation in CpG, CHG and</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> CHH context</span></pre>
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