[med-svn] [blasr] 08/12: Finalize manpage for samtoh5

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif-guest pushed a commit to branch master
in repository blasr.

commit eb7e9fdb8625225d7072b7ef599be9beafbc4021
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Jul 29 23:45:30 2015 -0700

    Finalize manpage for samtoh5
---
 debian/samtoh5.1 | 71 +++++++++++++++++++++++++++-----------------------------
 1 file changed, 34 insertions(+), 37 deletions(-)

diff --git a/debian/samtoh5.1 b/debian/samtoh5.1
index 3c6b0a1..3880048 100644
--- a/debian/samtoh5.1
+++ b/debian/samtoh5.1
@@ -1,56 +1,53 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
 .TH SAMTOH5 "1" "July 2015" "samtoh5 3ca7fe8" "User Commands"
 .SH NAME
-samtoh5 \- description of program
-.SH DESCRIPTION
-samtoh5 Converts in.sam file to out.cmp.h5 file.
-.PP
-usage: samtoh5 in.sam reference.fasta out.cmp.h5 [options]
-.IP
-in.sam
-.IP
+samtoh5 \- convert a SAM file to cmp.h5 format
+.SH SYNOPSIS
+.B samtoh5 
+.I in.sam
+.I reference.fasta
+.I out.cmp.h5
+.RI [ options ]
+.SH OPTIONS
+.TP
+.I in.sam
 Input SAM file.
-.IP
-reference.fasta
-.IP
+.TP
+.I reference.fasta
 Reference used to generate reads.
-.IP
-out.cmp.h5
-.IP
+.TP
+.I out.cmp.h5
 Output cmp.h5 file.
-.HP
-\fB\-smrtTitle\fR
-.IP
+.TP
+.B \-smrtTitle
 Use this option when converting alignments generated from reads
-produced by the pls2fasta from bas.h5 files by parsing read
-coordinates from the SMRT read title.  The title is in the
+produced by the
+.BR pls2fasta (1)
+from bas.h5 files by parsing read
+coordinates from the SMRT read title. The title is in the
 format \fI\,/name/hole/coordinates\/\fP, where coordinates are in the
 format \ed+_\ed+, and represent the interval of the read that was
 aligned.
-.HP
-\fB\-readType\fR value
-.IP
+.TP
+.BI \-readType \0value
 Set the read type: 'standard', 'strobe', 'CCS', or 'cDNA'
-.HP
-\fB\-verbosity\fR value
-.IP
+.TP
+.BI \-verbosity \0value
 Set desired verbosity.
-.HP
-\fB\-useShortRefName\fR
-.IP
-Use abbreviated reference names obtained from file.sam instead
-of using full names from reference.fasta.
-.HP
-\fB\-copyQVs\fR
-.IP
+.TP
+.B \-useShortRefName
+Use abbreviated reference names obtained from \fIfile.sam\fR instead
+of using full names from \fIreference.fasta\fR.
+.TP
+.B \-copyQVs
 Copy all QVs available in the SAM file into the cmp.h5 file.
 This includes things like InsertionQV and DeletionTag.
-.IP
+.SH NOTES
 Because SAM has optional tags that have different meanings in different
 programs, careful usage is required in order to have proper output. The
 "xs" tag in bwa\-sw is used to show the suboptimal score, but in PacBio SAM
-(blasr) it is defined as the start in the query sequence of the alignment.
-When "\-smrtTitle" is specified, the xs tag is ignored, but when it is not
+.RB ( blasr (1))
+it is defined as the start in the query sequence of the alignment.
+When \fB\-smrtTitle\fR is specified, the xs tag is ignored, but when it is not
 specified, the coordinates given by the xs and xe tags are used to define
 the interval of a read that is aligned. The CIGAR string is relative to
 this interval.

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.git