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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/marginphase">Debian Med / marginphase</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/marginphase/-/commit/a37c55ddbccb8f65d665b02ddd3265c51daa03a1">a37c55dd</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-07-03T08:44:29+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add metadata and description
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<h4>2 changed files:</h4>
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
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+
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/marginphase/-/commit/a37c55ddbccb8f65d665b02ddd3265c51daa03a1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,3 +18,14 @@ Architecture: any</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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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">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Description: simultaneous haplotyping and genotyping</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> MarginPhase is a program for simultaneous haplotyping and genotyping.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> It is an experimental, open source implementation written in C and</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> developed to work primarily with nanopore data. The MarginPhase workflow</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> includes an alignment summation step. This differentiates it from WhatsHap,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> which performs a local realignment around analyzed sites. MarginPhase can</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> also phase genotypic variants simultaneously after filtering out the sites</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> that are likely homozygous. MarginPhase’s output includes a BAM which</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> encodes the phasing of each read, including which phase set it is in, </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> which haplotype it belongs to, and what of the aligned portion falls </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> into each phase set. Reads which span a phase set boundary have information </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> for both encoded in them.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"></span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/marginphase/-/commit/a37c55ddbccb8f65d665b02ddd3265c51daa03a1#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Author: Jana Ebler and Marina Haukness and Trevor Pesout and Tobias Marschall and Benedict Paten </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: Haplotype-aware diplotyping from noisy long reads</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Journal: Genome Biol</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Year: 2019</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Volume: 20</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Number: 116</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Pages: </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> DOI: https://doi.org/10.1186/s13059-019-1709-0</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> PMID:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1709-0</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> eprint: </span></pre>
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