[med-svn] r19849 - trunk/packages/sumatra/trunk/debian

[Andreas Tille]

Author: tille
Date: 2015-08-05 19:14:30 +0000 (Wed, 05 Aug 2015)
New Revision: 19849

Added:
   trunk/packages/sumatra/trunk/debian/manpages
   trunk/packages/sumatra/trunk/debian/sumatra.1
Log:
Add manpage


Added: trunk/packages/sumatra/trunk/debian/manpages
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--- trunk/packages/sumatra/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/sumatra/trunk/debian/manpages	2015-08-05 19:14:30 UTC (rev 19849)
@@ -0,0 +1 @@
+debian/*.1

Added: trunk/packages/sumatra/trunk/debian/sumatra.1
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--- trunk/packages/sumatra/trunk/debian/sumatra.1	                        (rev 0)
+++ trunk/packages/sumatra/trunk/debian/sumatra.1	2015-08-05 19:14:30 UTC (rev 19849)
@@ -0,0 +1,76 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
+.TH SUMATRA "1" "August 2015" "sumatra 1.0.03" "User Commands"
+.SH NAME
+sumatra \- fast and exact comparison and clustering of sequences
+.SH SYNOPSIS
+.B sumatra
+\fI[options] <dataset1> [dataset2]\fR
+.SH DESCRIPTION
+Sumatra computes all the pairwise LCS (Longest Common Subsequence) scores
+of one nucleotide dataset or between two nucleotide datasets.
+.SH OPTIONS
+.TP
+\fB\-h\fR
+[H]elp \- print <this> help
+.TP
+\fB\-l\fR
+Reference sequence length is the shortest.
+.TP
+\fB\-L\fR
+Reference sequence length is the largest.
+.TP
+\fB\-a\fR
+Reference sequence length is the alignment length (default).
+.TP
+\fB\-n\fR
+Score is normalized by reference sequence length (default).
+.TP
+\fB\-r\fR
+Raw score, not normalized.
+.TP
+\fB\-d\fR
+Score is expressed in distance (default: score is expressed in similarity).
+.TP
+\fB\-t\fR \fI##.##\fR
+Score threshold. If the score is normalized and expressed in similarity (default),
+it is an identity, e.g. 0.95 for an identity of 95%. If the score is normalized
+and expressed in distance, it is (1.0 \- identity), e.g. 0.05 for an identity of 95%.
+If the score is not normalized and expressed in similarity, it is the length of the
+Longest Common Subsequence. If the score is not normalized and expressed in distance,
+it is (reference length \- LCS length).
+.br
+Only sequence pairs with a similarity above ##.## are printed. Default: 0.00
+(no threshold).
+.TP
+\fB\-p\fR \fI##\fR
+Number of threads used for computation (default=1).
+.TP
+\fB\-g\fR
+n's are replaced with a's (default: sequences with n's are discarded).
+.TP
+\fB\-x\fR
+Adds four extra columns with the count and length of both sequences.
+.TP
+\fIdataset1\fR
+(First argument) the nucleotide dataset to analyze
+.TP
+\fIdataset2\fR
+(Second argument) optionally the second nucleotide dataset
+.SH RESULTS
+Results table description
+.br
+column 1 : Identifier sequence 1
+.br
+column 2 : Identifier sequence 2
+.br
+column 3 : Score
+.br
+column 4 : Count of sequence 1  (only with option \fB\-x\fR)
+.br
+column 5 : Count of sequence 2  (only with option \fB\-x\fR)
+.br
+column 6 : Length of sequence 1 (only with option \fB\-x\fR)
+.br
+column 7 : Length of sequence 2 (only with option \fB\-x\fR)
+.SH SEE ALSO
+http://metabarcoding.org/sumatra