debian/changelog

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

debian/manpages

+debian/*.1

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

+.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.