This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository libsmithwaterman.
commit 7aafda632e7ad59f0cfa821ef79f872191f7a5e4 Author: Andreas Tille <[email protected]> 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 new file mode 100644 index 0000000..544569c --- /dev/null +++ b/debian/smithwaterman.1 @@ -0,0 +1,47 @@ +.\" 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libsmithwaterman.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
