[med-svn] [libsmithwaterman] 03/03: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository libsmithwaterman.

commit 7aafda632e7ad59f0cfa821ef79f872191f7a5e4
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 22 16:47:44 2016 +0200

    Add manpage
---
 debian/manpages        |  1 +
 debian/smithwaterman.1 | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+)

diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/smithwaterman.1 b/debian/smithwaterman.1
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index 0000000..544569c
--- /dev/null
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+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH SMITHWATERMAN "1" "June 2016" "smithwaterman 0.0+20151117" "User Commands"
+.SH NAME
+smithwaterman \- determine similar regions between two strings or nucleotide or protein sequences
+.SH SYNOPSIS
+.B smithwaterman
+[options] <reference sequence> <query sequence>
+.SH DESCRIPTION
+The Smith–Waterman algorithm performs local sequence alignment; that is,
+for determining similar regions between two strings or nucleotide or
+protein sequences. Instead of looking at the total sequence, the
+Smith–Waterman algorithm compares segments of all possible lengths and
+optimizes the similarity measure.
+.SH OPTIONS
+.TP
+\fB\-m\fR, \fB\-\-match\-score\fR
+the match score (default 10.0)
+.TP
+\fB\-n\fR, \fB\-\-mismatch\-score\fR
+the mismatch score (default \fB\-9\fR.0)
+.TP
+\fB\-g\fR, \fB\-\-gap\-open\-penalty\fR
+the gap open penalty (default 15.0)
+.TP
+\fB\-z\fR, \fB\-\-entropy\-gap\-open\-penalty\fR
+enable entropy scaling of the gap open penalty
+.TP
+\fB\-e\fR, \fB\-\-gap\-extend\-penalty\fR
+the gap extend penalty (default 6.66)
+.TP
+\fB\-r\fR, \fB\-\-repeat\-gap\-extend\-penalty\fR
+use repeat information when generating gap extension penalties
+.TP
+\fB\-b\fR, \fB\-\-bandwidth\fR
+bandwidth to use (default 0, or non\-banded algorithm)
+.TP
+\fB\-p\fR, \fB\-\-print\-alignment\fR
+print out the alignment
+.TP
+\fB\-R\fR, \fB\-\-reverse\-complement\fR
+report the reverse\-complement alignment if it scores better
+.PP
+When called with literal reference and query sequences, smithwaterman
+prints the cigar match positional string and the match position for the
+query sequence against the reference sequence.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

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