loadPulses1

Usage

Overview

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.