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)

loadPulses 3ca7fe8                                  July 2015                                      LOADPULSES(1)