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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/blends-team/med">Debian Blends Team / med</a>
</h3>
<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/blends-team/med/commit/215c63b0af845f9df7ecb5888272651ef8b4ec80">215c63b0</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-12-18T15:57:19Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove extra information from caftools
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#26b0fba1305554e48a6078ef69d0cfe948ad5765">
tasks/bio
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<h4>Changes:</h4>
<li id="26b0fba1305554e48a6078ef69d0cfe948ad5765">
<a href="https://salsa.debian.org/blends-team/med/commit/215c63b0af845f9df7ecb5888272651ef8b4ec80#26b0fba1305554e48a6078ef69d0cfe948ad5765"><strong>tasks/bio</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1812" 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">@@ -1812,28 +1812,6 @@ Recommends: r-cran-phytools</td>
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1812
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<td class="diff-line-num new_line" data-linenumber="1812" 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">
1812
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<pre style="margin: 0;"> <span id="LC1812" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: r-cran-treescape</span></span>
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<td class="diff-line-num old_line" data-linenumber="1813" 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">
1813
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<td class="diff-line-num new_line" data-linenumber="1813" 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">
1813
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<pre style="margin: 0;"> <span id="LC1813" class="line" lang="mosel"></span>
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<td class="diff-line-num old_line" data-linenumber="1814" 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">
1814
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<td class="diff-line-num new_line" data-linenumber="1814" 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">
1814
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1814" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: caftools</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1815" 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">
1815
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<td class="diff-line-num new_line old" data-linenumber="1815" 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="LC1815" class="line" lang="mosel"><span class="s1" style="color: #d14;">Homepage: http://www.sanger.ac.uk/Software/formats/CAF/userguide.shtml</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1816" 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">
1816
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<td class="diff-line-num new_line old" data-linenumber="1815" 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="LC1816" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: Free for non-commercial purposes</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1817" 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">
1817
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<td class="diff-line-num new_line old" data-linenumber="1815" 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="LC1817" class="line" lang="mosel"><span class="s1" style="color: #d14;">Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk></span></span>
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<td class="diff-line-num old old_line" data-linenumber="1818" 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">
1818
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<td class="diff-line-num new_line old" data-linenumber="1815" 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="LC1818" class="line" lang="mosel"><span class="s1" style="color: #d14;">Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1819" 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">
1819
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<td class="diff-line-num new_line old" data-linenumber="1815" 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="LC1819" class="line" lang="mosel"><span class="s1" style="color: #d14;">Pkg-Description: Tools to maintain DNA sequence assemblies</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1820" 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">
1820
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<td class="diff-line-num new_line old" data-linenumber="1815" 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="LC1820" class="line" lang="mosel"><span class="s1" style="color: #d14;"> This is V2 of the CAF (Common Assembly Format) C-tools. It comprises</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1821" 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">
1821
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<td class="diff-line-num new_line old" data-linenumber="1815" 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="LC1821" class="line" lang="mosel"><span class="s1" style="color: #d14;"> a set of libraries and programs for manipulating DNA sequence</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1822" 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">
1822
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<pre style="margin: 0;">-<span id="LC1822" class="line" lang="mosel"><span class="s1" style="color: #d14;"> assemblies using CAF files.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1823" 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">
1823
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<pre style="margin: 0;">-<span id="LC1823" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1824" 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">
1824
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<pre style="margin: 0;">-<span id="LC1824" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The CAF specification can be found at:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1825" 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="LC1825" class="line" lang="mosel"><span class="s1" style="color: #d14;"> http://www.sanger.ac.uk/Software/formats/CAF/</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1826" 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">
1826
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<pre style="margin: 0;">-<span id="LC1826" class="line" lang="mosel"><span class="s1" style="color: #d14;">Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1827" 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">
1827
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<pre style="margin: 0;">-<span id="LC1827" class="line" lang="mosel"><span class="s1" style="color: #d14;"> maintains a package called bio-linux-assembly-conversion-tools which</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1828" 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">
1828
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<pre style="margin: 0;">-<span id="LC1828" class="line" lang="mosel"><span class="s1" style="color: #d14;"> contains caftools and roche2gap in one package with the following</span></span>
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1829
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<pre style="margin: 0;">-<span id="LC1829" class="line" lang="mosel"><span class="s1" style="color: #d14;"> description:</span></span>
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1830
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<pre style="margin: 0;">-<span id="LC1830" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1831" 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">
1831
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<pre style="margin: 0;">-<span id="LC1831" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Conversion tools for handling 454 assemblies.</span></span>
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1832
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<pre style="margin: 0;">-<span id="LC1832" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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<pre style="margin: 0;">-<span id="LC1833" class="line" lang="mosel"><span class="s1" style="color: #d14;"> This package contains code from different authors that allow sequence</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1834" 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">
1834
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<pre style="margin: 0;">-<span id="LC1834" class="line" lang="mosel"><span class="s1" style="color: #d14;"> assemblies to be converted into formats such as CAF (Common Assembly</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1835" 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">
1835
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<td class="diff-line-num new_line old" data-linenumber="1815" 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="LC1835" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Format) or GAP4. This package includes tools to convert assemblies</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1836" 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">
1836
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<pre style="margin: 0;">-<span id="LC1836" class="line" lang="mosel"><span class="s1" style="color: #d14;"> from Newbler'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">ace</span> <span class="n" style="color: #333;">format</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">loading</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">gap4</span> <span class="n" style="color: #333;">assembly</span><span class="p">.</span></span>
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<td class="diff-line-num old_line" data-linenumber="1837" 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">
1837
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1815
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<pre style="margin: 0;"> <span id="LC1815" class="line" lang="mosel"></span>
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<td class="diff-line-num old_line" data-linenumber="1838" 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">
1838
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<td class="diff-line-num new_line" data-linenumber="1816" 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">
1816
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<pre style="margin: 0;"> <span id="LC1816" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: roche454ace2caf</span></span>
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<td class="diff-line-num old_line" data-linenumber="1839" 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">
1839
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<td class="diff-line-num new_line" data-linenumber="1817" 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">
1817
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<pre style="margin: 0;"> <span id="LC1817" class="line" lang="mosel"><span class="s1" style="color: #d14;">Homepage: http://genome.imb-jena.de/software/roche454ace2caf/</span></span>
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