[med-svn] [blasr] 11/12: Finalize loadPulses manpage

[Afif Elghraoui]

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commit d9d77401824c0c7b4af7e43d1f9c90c24a50b69b
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu Jul 30 00:29:44 2015 -0700

    Finalize loadPulses manpage
---
 debian/loadPulses.1 | 96 ++++++++++++++++++++++++-----------------------------
 1 file changed, 44 insertions(+), 52 deletions(-)

diff --git a/debian/loadPulses.1 b/debian/loadPulses.1
index be6d5e9..0759873 100644
--- a/debian/loadPulses.1
+++ b/debian/loadPulses.1
@@ -1,75 +1,67 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
 .TH LOADPULSES "1" "July 2015" "loadPulses 3ca7fe8" "User Commands"
 .SH NAME
-loadPulses \- description of program
+loadPulses \- load sequencing pulse information
+.SH SYNOPSIS
+.B loadPulses
+.I basFileName
+.I cmpFileName
+.RI [ options ]
 .SH DESCRIPTION
-loadPulses Loads pulse information such as inter pulse distance, or quality
-.IP
-information into the cmp.h5 file. This allows one to analyze kinetic
-and quality information by alignment column.
-.PP
-usage: loadPulses basFileName cmpFileName [options]
-.IP
-basFileName
-.IP
+.B loadPulses
+loads sequencing pulse information such as inter-pulse distance or quality
+information into the cmp.h5 file.
+This allows one to analyze kinetic and quality information by alignment column.
+.SH OPTIONS
+.TP
+.I basFileName
 The input {bas,pls}.h5 or input.fofn.
-.IP
-cmpFileName
-.IP
+.TP
+.I cmpFileName
 The cmp.h5 file to load pulse information into.
-.HP
-\fB\-metrics\fR value
-.IP
+.TP
+.BI \-metrics \0value
 A comma separated list of metrics (with no spaces).
+.RS
+.TP
 Valid options are:
-WhenStarted,QualityValue,InsertionQV,MergeQV,
-DeletionQV,DeletionTag,SubstitutionTag,SubstitutionQV,
-PreBaseFrames,IPD,StartFrame,PulseWidth,
-WidthInFrames,Light,pkmid,ClassifierQV,
-PulseIndex
+WhenStarted, QualityValue, InsertionQV, MergeQV,
+DeletionQV, DeletionTag, SubstitutionTag, SubstitutionQV, PreBaseFrames, IPD,
+StartFrame, PulseWidth, WidthInFrames, Light, pkmid, ClassifierQV, PulseIndex
+.TP
 Default options are:
-QualityValue,ClassifierQV,StartFrame,PulseWidth,
-WidthInFrames,pkmid,IPD
-.HP
-\fB\-failOnMissingData\fR
-.IP
+QualityValue, ClassifierQV, StartFrame, PulseWidth,
+WidthInFrames, pkmid, IPD
+.RE
+.TP
+.B \-failOnMissingData
 Exit if any data fields are missing from the bas.h5 or pls.h5
 input that are required to load a metric. Defualt is a warning.
-.HP
-\fB\-byread\fR
-.IP
+.TP
+.B \-byread
 Load pulse information by read rather than buffering metrics.
-.HP
-\fB\-bymetric\fR
-.IP
+.TP
+.B \-bymetric
 Load pulse information by metric rather than by read. This uses
 more memory than \fB\-byread\fR, but can be faster.
-.HP
-\fB\-maxElements\fR value
-.IP
+.TP
+.BI \-maxElements \0value
 Set a limit on the size of pls/bas file to buffer in with
 \fB\-bymetric\fR (default value: maximum int). Use \fB\-byread\fR if the limit
 is exceeded.
-.HP
-\fB\-maxMemory\fR value
-.IP
+.TP
+.BI \-maxMemory \0value
 Set a limit (in GB) on the memory to buffer data with \fB\-bymetric\fR
 (default value: 4 GB). Use \fB\-byread\fR if the limit is exceeded.
-.HP
-\fB\-metaNElements\fR value
-.IP
+.TP
+.BI \-metaNElements \0value
 Set number of elements in meta data cache for reading
 bas/bax/pls.h5 file.
-.HP
-\fB\-rawNElements\fR value
-.IP
-Set number of elements in raw data cache for reading
-bas/bax/pls.h5 file.
-.HP
-\fB\-rawChunkSize\fR value
-.IP
-Set chunk size of raw data cache for reading bas/bax/pls.h5
-file.
+.TP
+.BI \-rawNElements value
+Set number of elements in raw data cache for reading the bas/bax/pls.h5 file.
+.TP
+.BI \-rawChunkSize \0value
+Set chunk size of raw data cache for reading the bas/bax/pls.h5 file.
 .SH SEE ALSO
 .BR blasr (1)
 .BR pls2fasta (1)

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