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)