[med-svn] [Git][med-team/kissplice][master] Use CMake-installed manpage

[François Gindraud (@fgindraud)]

François Gindraud pushed to branch master at Debian Med / kissplice


Commits:
fa5fcda8 by Francois Gindraud at 2022-04-06T14:34:54+02:00
Use CMake-installed manpage

An old manpage was included in the packaging directory and overwrote the
upstream one.
Upstream now installs a manpage during cmake install in the correct
directory.
This uncompressed manpage should be compressed by dh_compress to fit the
packaging guidelines.

- - - - -


3 changed files:

- debian/changelog
- − debian/kissplice.1
- − debian/kissplice.manpages


Changes:

=====================================
debian/changelog
=====================================
@@ -11,6 +11,7 @@ kissplice (2.6.1-1) UNRELEASED; urgency=medium
   * Remove gcc10 patch
   * Replace redirection script with symlink to bcalm
   * New upstream version
+  * Use generated doc and upsteam manpage
 
  -- Andreas Tille <tille at debian.org>  Fri, 01 Apr 2022 11:44:54 +0200
 


=====================================
debian/kissplice.1 deleted
=====================================
@@ -1,87 +0,0 @@
-.TH KISSPLICE "1" "June 2013" "kissplice 1.8.3-1" "User Commands"
-.SH NAME
-kissplice \- detection of polymorphisms in RNA-seq data.
-.SH SYNOPSIS
-kissplice \-h
-.br
-kissplice [OPTION] [\-r READFILES]
-.SH DESCRIPTION
-Detects alternative splicing events and other kinds of polymorphisms from
-READFILES (in FASTA or FASTQ format).
-.SH OPTIONS
-.TP
-.B
-\-h, \-\-help
-Show this help message and exit.
-.TP
-\fB\-r\fR READFILES
-Input fasta/q read files (multiple, such as "\-r file1 \fB\-r\fR file2...").
-.TP
-\fB\-k\fR KVAL
-k\-mer size (default=25).
-.TP
-\fB\-l\fR LLMAX
-Maximal length of the shorter path (default: 2k\-1).
-.TP
-\fB\-m\fR LL_MIN
-Minimum length of the shorter path (default 2k\-8).
-.TP
-\fB\-M\fR UL_MAX
-Maximum length of the longest path (default 1000),
-skipped exons longer than UL_MAX are not reported.
-.TP
-\fB\-g\fR GRAPH_PREFIX
-Path and prefix to pre\-built de Bruijn graph (suffixed
-by .edges/.nodes) if jointly used with \fB\-r\fR, graph used
-to find bubbles and reads used for quantification.
-.TP
-\fB\-o\fR OUT_DIR
-Path to store the results (default = ./results).
-.TP
-\fB\-d\fR PATH_TO_TMP
-Specific directory (absolute path) where to build
-temporary files (default temporary directory otherwise).
-.TP
-\fB\-t\fR NBPROCS
-Number of cores (must be <= number of physical cores).
-.TP
-\fB\-s\fR
-Don't output SNPs (saves time).
-.TP
-\fB\-v\fR
-Verbose mode.
-.TP
-\fB\-u\fR
-Keep the nodes/edges file for unfinished bccs.
-.TP
-\fB\-c\fR MIN_COV
-Discard k\-mers tha are present strictly less than this
-number of times in the dataset.
-(default 2).
-.TP
-\fB\-C\fR MIN_RELATIVE_COV
-Discard edges with relative coverage
-below MIN_RELATIVE_COV expressed as a percentage in [0,1).
-(default 0.02).
-.TP
-\fB\-z\fR GENOME_SIZE
-Estimated number of nodes in the De-Bruin Graph.
-(default = 1000000000).
-.TP
-\fB\-e\fR MIN_EDIT_DIST
-Classify as inexact repeats those bubbles whose paths'
-edit distance is smaller than MIN_EDIT_DIST
-(default 3).
-.TP
-\fB\-y\fR MAX_CYCLES
-Maximal number of bubble enumerations in each bcc. If
-exceeded, no bubble is output for the bcc (default
-10000).
-.TP
-\fB\-\-timeout\fR TIMEOUT
-Max amount of time (in seconds) spent for enumerating
-bubbles in each bcc. If exceeded, no bubble is output
-for the bcc (default 900).
-.TP
-\fB\-\-version\fR
-Display program's version number and exit.


=====================================
debian/kissplice.manpages deleted
=====================================
@@ -1 +0,0 @@
-debian/kissplice.1



View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/commit/fa5fcda8a8bc12468da025775532ac5af09a3613

-- 
View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/commit/fa5fcda8a8bc12468da025775532ac5af09a3613
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