[med-svn] [Git][med-team/surpyvor][master] 4 commits: Add python3-upsetplot to Depends

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / surpyvor


Commits:
62f3a35c by Nilesh Patra at 2021-07-13T19:43:22+05:30
Add python3-upsetplot to Depends

- - - - -
55e6f42d by Nilesh Patra at 2021-07-13T14:20:12+00:00
Add manpage

- - - - -
84af058b by Nilesh Patra at 2021-07-13T19:56:27+05:30
d/control: Minor fix

- - - - -
530f6ff6 by Nilesh Patra at 2021-07-13T19:57:10+05:30
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/createmanpages
- + debian/manpages
- + debian/surpyvor.1


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-surpyvor (0.5-1) UNRELEASED; urgency=medium
+surpyvor (0.5-1) unstable; urgency=medium
 
   * Initial release (Closes: #990883)
 
- -- Steffen Moeller <moeller at debian.org>  Sat, 10 Jul 2021 00:01:07 +0200
+ -- Steffen Moeller <moeller at debian.org>  Tue, 13 Jul 2021 19:52:30 +0530


=====================================
debian/control
=====================================
@@ -21,13 +21,14 @@ Depends:
  python3-cyvcf2,
  python3-matplotlib-venn,
  survivor,
+ python3-upsetplot,
  ${misc:Depends},
  ${python3:Depends},
 Description: modification of VCF files with SURVIVOR
  SURVIVOR is a tool set for simulating/evaluating
- structural variantions, merging and comparing SVs within
+ structural variations, merging and comparing SVs within
  and among samples, and includes various methods to
- reformat or summarize structural variantions.
+ reformat or summarize structural variations.
  .
  This package provides a Python wrapper to help with its
  integration in various Python-based workflows.


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,29 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=surpyvor
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1


=====================================
debian/surpyvor.1
=====================================
@@ -0,0 +1,39 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
+.TH SURPYVOR "1" "July 2021" "surpyvor 0.5" "User Commands"
+.SH NAME
+surpyvor \- modification of VCF files with SURVIVOR
+.SH DESCRIPTION
+usage: surpyvor [\-h] [\-v] {merge,highsens,highconf,prf,venn,upset} ...
+.PP
+A wrapper around SURVIVOR, with convenience functions.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+Print version and quit.
+.SS "[sub-commands]:"
+.IP
+{merge,highsens,highconf,prf,venn,upset}
+.TP
+merge
+merging vcf files of SVs
+.TP
+highsens
+get union of SV vcfs
+.TP
+highconf
+get intersection of SV vcfs
+.TP
+prf
+calculate precision, recall and F\-measure
+.TP
+venn
+Make venn diagram for 2 or 3 SV vcf files
+.TP
+upset
+Make upset plot for multiple SV vcf files
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.



View it on GitLab: https://salsa.debian.org/med-team/surpyvor/-/compare/38ffe8416adc05ed856d761b844a04f258559cda...530f6ff641ddec7bad78fec429127783e289a0af

-- 
View it on GitLab: https://salsa.debian.org/med-team/surpyvor/-/compare/38ffe8416adc05ed856d761b844a04f258559cda...530f6ff641ddec7bad78fec429127783e289a0af
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