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.
SEE ALSO
blasr(1) pls2fasta(1) samFilter(1) samtoh5(1) samtom4(1) sawriter(1) sdpMatcher(1) toAfg(1)