.TH LOADPULSES "1" "July 2015" "loadPulses 3ca7fe8" "User Commands"
.SH NAME
loadPulses \- load sequencing pulse information
.SH SYNOPSIS
.B loadPulses
.I basFileName
.I cmpFileName
.RI [ options ]
.SH DESCRIPTION
.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.
.TP
.I cmpFileName
The cmp.h5 file to load pulse information into.
.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
.TP
Default options are:
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.
.TP
.B \-byread
Load pulse information by read rather than buffering metrics.
.TP
.B \-bymetric
Load pulse information by metric rather than by read. This uses
more memory than \fB\-byread\fR, but can be faster.
.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.
.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.
.TP
.BI \-metaNElements \0value
Set number of elements in meta 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)
.BR samFilter (1)
.BR samtoh5 (1)
.BR samtom4 (1)
.BR sawriter (1)
.BR sdpMatcher (1)
.BR toAfg (1)