[med-svn] [blasr] 06/12: Finalize sawriter manpage

[Afif Elghraoui]

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commit 1f723d387b1f81ebb6b59648a0a7a6715106c6b1
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Jul 29 23:20:52 2015 -0700

    Finalize sawriter manpage
---
 debian/sawriter.1 | 57 ++++++++++++++++++++++++++++++++++---------------------
 1 file changed, 35 insertions(+), 22 deletions(-)

diff --git a/debian/sawriter.1 b/debian/sawriter.1
index a546e69..ea3af56 100644
--- a/debian/sawriter.1
+++ b/debian/sawriter.1
@@ -1,41 +1,54 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
 .TH SAWRITER "1" "July 2015" "sawriter 3ca7fe8" "User Commands"
 .SH NAME
-sawriter \- description of program
-.SH DESCRIPTION
-usage: sawriter saOut fastaIn [fastaIn2 fastaIn3 ...] [\-blt p] [\-larsson] [\-4bit] [\-manmy] [\-kar]
-.TP
-or
-sawriter fastaIn  (writes to fastIn.sa).
-\fB\-blt\fR p      Build a lookup table on prefixes of length 'p'. This speeds
-.IP
+sawriter \- generate suffix arrays for nucleotide sequences
+.SH SYNOPSIS
+.B sawriter
+.I saOut \0fastaIn
+.RI [ fastaIn2
+.IR fastaIn3 \0...]
+.RB [ \-blt
+.IR p ]
+.RB [ \-4bit ]
+.RB [ \-larsson | \-manmy | \-kar | \-mafe | \-welter ]
+.P
+.B sawriter
+.I fastaIn
+.R (writes to fastaIn.sa)
+.SH OPTIONS
+.TP
+.BI \-blt \0p
+Build a lookup table on prefixes of length \fIp\fR. This speeds
 up lookups considerably (more than the LCP table), but misses matches
-less than p when searching.
+less than \fIp\fR when searching.
 .TP
-\fB\-4bit\fR
+.B \-4bit
 Read in (one) fasta file as a compressed sequence file.
 .TP
-\fB\-larsson\fR
+.B Methods
+.RS
+.B \-larsson
 (default)  Uses the method of Larsson and Sadakane to build the array.
 .TP
-\fB\-mamy\fR
+.B \-mamy
 Uses the method of MAnber and MYers to build the array (slower than larsson,
-.IP
 and produces the same result. This is mainly for double checking
 the correctness of larsson).
 .TP
-\fB\-kark\fR
-Use Karkkainen DS3 method for building the suffix array.  This will probably be more
-slow than larsson, but takes only an extra N/(sqrt 3) extra space.
+.B \-kark
+Use Karkkainen DS3 method for building the suffix array.
+This will probably be slower than larsson, but takes only an extra
+N/(sqrt 3) extra space.
 .TP
-\fB\-mafe\fR
+.B \-mafe
 (disabled for now!) Use the lightweight construction algorithm from Manzini and Ferragina
 .TP
-\fB\-welter\fR
-Use lightweight (sort of light) suffix array construction.  This is a bit more slow than
-normal larsson.
+.B \-welter
+Use lightweight (sort of light) suffix array construction.
+This is a bit more slow than normal larsson.
+.RE
 .TP
-\fB\-welterweight\fR N use a difference cover of size N for building the suffix array.
+.BI \-welterweight \0N
+use a difference cover of size \fIN\fR for building the suffix array.
 Valid values are 7,32,64,111, and 2281.
 .SH SEE ALSO
 .BR blasr (1)

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