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loadPulses - load sequencing pulse information


loadPulses basFileName cmpFileName [options]


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.


The input {bas,pls}.h5 or input.fofn.

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,

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.

Load pulse information by read rather than buffering metrics.

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.

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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