This is the command loadPulses that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
loadPulses - load sequencing pulse information
SYNOPSIS
loadPulses basFileName cmpFileName [options]
DESCRIPTION
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.
OPTIONS
basFileName
The input {bas,pls}.h5 or input.fofn.
cmpFileName
The cmp.h5 file to load pulse information into.
-metrics value
A comma separated list of metrics (with no spaces).
Valid options are:
WhenStarted, QualityValue, InsertionQV, MergeQV, DeletionQV, DeletionTag,
SubstitutionTag, SubstitutionQV, PreBaseFrames, IPD, StartFrame, PulseWidth,
WidthInFrames, Light, pkmid, ClassifierQV, PulseIndex
Default options are:
QualityValue, ClassifierQV, StartFrame, PulseWidth, WidthInFrames, pkmid,
IPD
-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.
-byread
Load pulse information by read rather than buffering metrics.
-bymetric
Load pulse information by metric rather than by read. This uses more memory than
-byread, but can be faster.
-maxElements value
Set a limit on the size of pls/bas file to buffer in with -bymetric (default value:
maximum int). Use -byread if the limit is exceeded.
-maxMemory value
Set a limit (in GB) on the memory to buffer data with -bymetric (default value: 4
GB). Use -byread if the limit is exceeded.
-metaNElements value
Set number of elements in meta data cache for reading bas/bax/pls.h5 file.
-rawNElementsvalue
Set number of elements in raw data cache for reading the bas/bax/pls.h5 file.
-rawChunkSize value
Set chunk size of raw data cache for reading the bas/bax/pls.h5 file.
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