[med-svn] [Git][med-team/kineticstools][master] added a patch to restore an array in the man

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / kineticstools


Commits:
f4467cb5 by Etienne Mollier at 2020-04-20T23:03:58+02:00
added a patch to restore an array in the man

- - - - -


2 changed files:

- + debian/patches/man-align-cols.patch
- debian/patches/series


Changes:

=====================================
debian/patches/man-align-cols.patch
=====================================
@@ -0,0 +1,40 @@
+Description: Align columns of the first tabular
+ There are three tabulars in doc/manual.rst, but only two are rendered in various contexts:
+   - sphinx-build -b man,
+   - rst2man,
+   - the Github renderer.
+ .
+ This slight modification should bring it back to rendered documentations.
+Author: Étienne Mollier <etienne.mollier at mailoo.org>
+Bug: https://github.com/PacificBiosciences/kineticsTools/pull/74
+Last-Update: 2020-04-20
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- kineticstools.orig/doc/manual.rst
++++ kineticstools/doc/manual.rst
+@@ -119,11 +119,11 @@
+ 
+ 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.
+ 
+-================  ===========
+-Column      Description
+-================  ===========
+-seqid     Fasta contig name
+-source            Name of tool -- 'kinModCall'
++================        ===========
++Column                  Description
++================        ===========
++seqid                   Fasta contig name
++source                  Name of tool -- 'kinModCall'
+ 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
+ start                   Modification position on contig
+ end                     Modification position on contig
+@@ -131,7 +131,7 @@
+ strand                  Sample strand containing modification
+ phase                   Not applicable
+ 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.
+-================  ===========
++================        ===========
+ 
+ modifications.csv
+ -----------------


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ deactivate-tests-requiring-unavailable-data.patch
 spelling.patch
 #ignore_h5py_deprecation_warnings_in_test.patch
 tests2to3.patch
+man-align-cols.patch



View it on GitLab: https://salsa.debian.org/med-team/kineticstools/-/commit/f4467cb594faa667b0b7f82b47cee24893595b88

-- 
View it on GitLab: https://salsa.debian.org/med-team/kineticstools/-/commit/f4467cb594faa667b0b7f82b47cee24893595b88
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