[med-svn] [blasr] 10/12: Finalize manpage for pls2fasta

[Afif Elghraoui]

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commit 6ea9f9e1199a4e544147664b7d9ce9fdc5bab581
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu Jul 30 00:20:13 2015 -0700

    Finalize manpage for pls2fasta
---
 debian/pls2fasta.1 | 92 ++++++++++++++++++++++--------------------------------
 1 file changed, 38 insertions(+), 54 deletions(-)

diff --git a/debian/pls2fasta.1 b/debian/pls2fasta.1
index 64ad554..0540bc7 100644
--- a/debian/pls2fasta.1
+++ b/debian/pls2fasta.1
@@ -1,78 +1,62 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
 .TH PLS2FASTA "1" "July 2015" "pls2fasta 3ca7fe8" "User Commands"
 .SH NAME
-pls2fasta \- description of program
+pls2fasta \- convert plx.h5/bax.h5/fofn files to fasta or fastq files
+.SH SYNOPSIS
+.B pls2fasta
+.I in.bax.h5
+.I out.fasta
+.RI [ options ]
 .SH DESCRIPTION
-pls2fasta Converts plx.h5/bax.h5/fofn files to fasta or fastq files. Although
-.IP
-fasta files are provided with every run, they are not trimmed nor
+Although fasta files are provided with every run, they are not trimmed nor
 split into subreads. This program takes additional annotation
-information, such as the subread coordinates and high quality regions
+information, such as the subread coordinates and high quality regions,
 and uses them to create fasta sequences that are substrings of all
-bases called. Most of the time you will want to trim low quality
+bases called. Most of the time, you will want to trim low quality
 reads, so you should specify \fB\-trimByRegion\fR.
-.PP
-usage: pls2fasta in.bax.h5 out.fasta [options]
-.IP
-in.bax.h5
-.IP
+.SH OPTIONS
+.TP
+.I in.bax.h5
 Input plx.h5/bax.h5/fofn file.
-.IP
-out.fasta
-.IP
+.TP
+.I out.fasta
 Output fasta/fastq file.
-.HP
-\fB\-trimByRegion\fR
-.IP
+.TP
+.B \-trimByRegion
 Trim away low quality regions.
-.HP
-\fB\-maskByRegion\fR
-.IP
+.TP
+.B \-maskByRegion
 Mask low quality regions with 'N'.
-.HP
-\fB\-regionTable\fR value
-.IP
+.TP
+.BI \-regionTable \0value
 Optional HDF file with a \fI\,/PulseData/Regions\/\fP dataset.
-.HP
-\fB\-minSubreadLength\fR value
-.IP
+.TP
+.BI \-minSubreadLength \0value
 Do not write subreads less than the specified length.
-.HP
-\fB\-noSplitSubreads\fR
-.IP
+.TP
+.B \-noSplitSubreads
 Do not split reads on adapter sequences.
-.HP
-\fB\-holeNumber\fR
-.IP
+.TP
+.B \-holeNumber
 Only print this hole number (or list of numbers).
-.HP
-\fB\-fastq\fR
-.IP
+.TP
+.B \-fastq
 Print in FASTQ format with quality.
-.HP
-\fB\-ccs\fR
-.IP
-Print de novo CCS sequences
-.HP
-\fB\-lineLength\fR value
-.IP
+.TP
+.B \-ccs
+Print de novo circular consensus (ccs) sequences
+.TP
+.B \-lineLength \0value
 Specify fasta/fastq line length
-.HP
-\fB\-minReadScore\fR value
 .TP
+.BI \-minReadScore \0value
 Minimum read score to print a read.
-The score is a number
-.IP
-between 0 and 1000 and represents the expected accuracy
+The score is a number between 0 and 1000 and represents the expected accuracy
 percentage * 10. A typical value would be between 750 and 800.
 This does not apply to ccs reads.
-.HP
-\fB\-best\fR
-.TP
-If a CCS sequence exists, print this.
-Otherwise, print the
 .TP
-longestsubread.
+.B \-best
+If a ccs sequence exists, print this.
+Otherwise, print the longest subread.
 This does not support fastq.
 .SH SEE ALSO
 .BR blasr (1)

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