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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/kineticstools">Debian Med / kineticstools</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/kineticstools/-/commit/f4467cb594faa667b0b7f82b47cee24893595b88">f4467cb5</a></strong>
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<span>by Etienne Mollier</span>
<i>at 2020-04-20T23:03:58+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added a patch to restore an array in the man
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#9b375579c26dc26385e3a301324f792679fd3c22">
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+
debian/patches/man-align-cols.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9b375579c26dc26385e3a301324f792679fd3c22">
<a href="https://salsa.debian.org/med-team/kineticstools/-/commit/f4467cb594faa667b0b7f82b47cee24893595b88#9b375579c26dc26385e3a301324f792679fd3c22"><strong>debian/patches/man-align-cols.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Align columns of the first tabular</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> There are three tabulars in doc/manual.rst, but only two are rendered in various contexts:</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> - sphinx-build -b man,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> - rst2man,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> - the Github renderer.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> This slight modification should bring it back to rendered documentations.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Bug: https://github.com/PacificBiosciences/kineticsTools/pull/74</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">Last-Update: 2020-04-20</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kineticstools.orig/doc/manual.rst</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kineticstools/doc/manual.rst</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -119,11 +119,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> The auxiliary data column of the GFF file contains other statistics which may be useful downstream analysis or filtering. In particular the coverage level of the reads used to make the call, and +/- 20bp sequence context surrounding the site.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-================ ===========</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Column Description</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-================ ===========</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-seqid Fasta contig name</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-source Name of tool -- 'kinModCall'</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+================ ===========</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Column Description</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+================ ===========</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+seqid Fasta contig name</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+source Name of tool -- 'kinModCall'</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> type Modification type -- in identification mode this will be m6A, m4C, or m5C for identified bases, or the generic tag 'modified_base' if a kinetic event was detected that does not match a known modification signature</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> start Modification position on contig</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> end Modification position on contig</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -131,7 +131,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> strand Sample strand containing modification</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> phase Not applicable</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> attributes Extra fields relevant to base mods. IPDRatio is traditional IPDRatio, context is the reference sequence -20bp to +20bp around the modification, and coverage level is the number of IPD observations used after Mapping QV filtering and accuracy filtering. If the row results from an identified modification we also include an identificationQv tag with the from the modification identification procedure. identificationQv is the phred-transformed probability of an incorrect identification, for bases that were identified as having a particular modification. frac, fracLow, fracUp are the estimated fraction of molecules carrying the modification, and the 5% confidence intervals of the estimate. The methylated fraction estimation is a beta-level feature, and should only be used for exploratory purposes.</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-================ ===========</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+================ ===========</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> modifications.csv</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> -----------------</span></pre>
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<a href="https://salsa.debian.org/med-team/kineticstools/-/commit/f4467cb594faa667b0b7f82b47cee24893595b88#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -6,3 +6,4 @@ deactivate-tests-requiring-unavailable-data.patch</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">spelling.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">#ignore_h5py_deprecation_warnings_in_test.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">tests2to3.patch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">man-align-cols.patch</span></pre>
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