[med-svn] [Git][med-team/spoa][master] 3 commits: Add ITP bug

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / spoa


Commits:
006c9c02 by Andreas Tille at 2018-06-09T14:26:27+02:00
Add ITP bug

- - - - -
0b32c809 by Andreas Tille at 2018-06-09T15:22:05+02:00
Hardening

- - - - -
c852b74f by Andreas Tille at 2018-06-09T15:25:57+02:00
Add manpage

- - - - -


4 changed files:

- debian/changelog
- + debian/manpages
- debian/rules
- + debian/spoa.1


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
 spoa (1.1.3-1) UNRELEASED; urgency=medium
 
-  * Initial release (Closes: #xxx)
+  * Initial release (Closes: #901145)
 
  -- Andreas Tille <tille at debian.org>  Fri, 08 Jun 2018 13:20:51 +0200


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


=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -2,9 +2,10 @@
 
 # DH_VERBOSE := 1
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 DEB_CMAKE_EXTRA_FLAGS = -DCMAKE_BUILD_TYPE=Release \
-                        -Dspoa_build_executable=ON \
-                        -DBUILD_SHARED_LIBS=ON
+                        -Dspoa_build_executable=ON
 
 %:
 	dh $@


=====================================
debian/spoa.1
=====================================
--- /dev/null
+++ b/debian/spoa.1
@@ -0,0 +1,63 @@
+.TH SPOA "1" "June 2018" "spoa 1.1.3" "User Commands"
+.SH NAME
+spoa \- SIMD partial order alignment tool
+.SH SYNOPSIS
+.B spoa
+[options ...] <sequences>
+.SH DESCRIPTION
+Spoa (SIMD POA) is a c++ implementation of the partial order alignment
+(POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which
+is used to generate consensus sequences (as described in
+10.1093/bioinformatics/btg109). It supports three alignment modes: local
+(Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
+(overlap).
+.SH OPTIONS
+.HP
+<sequences>
+.IP
+input file in FASTA/FASTQ format containing sequences
+.IP
+.SS Optional
+.HP
+\fB\-m\fR, \fB\-\-match\fR <int>
+.IP
+default: 5
+score for matching bases
+.HP
+\fB\-x\fR, \fB\-\-mismatch\fR <int>
+.IP
+default: \fB\-4\fR
+score for mismatching bases
+.HP
+\fB\-g\fR, \fB\-\-gap\fR <int>
+.IP
+default: \fB\-8\fR
+gap penalty (must be negative)
+.HP
+\fB\-l\fR, \fB\-\-algorithm\fR <int>
+.IP
+default: 0
+alignment mode:
+.IP
+0 \- local (Smith\-Waterman)
+1 \- global (Needleman\-Wunsch)
+2 \- semi\-global
+.HP
+\fB\-r\fR, \fB\-\-result\fR <int>
+.IP
+default: 0
+result mode:
+.IP
+0 \- consensus
+1 \- multiple sequence alignment
+2 \- 0 & 1
+.HP
+\fB\-\-version\fR
+.IP
+prints the version number
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+prints the usage
+.SH AUTHOR
+This manpage was written by Andreas Tille 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/spoa/compare/2db4688bf392455991b9d6eb9387b8193bff640a...c852b74fe4b1ea72d47d74c1e722e5e0183a393e

-- 
View it on GitLab: https://salsa.debian.org/med-team/spoa/compare/2db4688bf392455991b9d6eb9387b8193bff640a...c852b74fe4b1ea72d47d74c1e722e5e0183a393e
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