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3. GS Amplicon Variant Analyzer Command Line Interface : 3.4 AVA-CLI Command Usage Statements : 3.4.8 load
3.4.8
load
 
    load -readGroup <read group name>
         -sffDir <SFF directory>
         -sffName <SFF file name>
         [-symLink <boolean>]
         [-alias <alias prefix for command interpreter>]
         [-file <file> [-format <format>]]
 
    load -readGroup <read group name>
         -analysisDir <analysis directory>
         -sffName <SFF file name>
         [-symLink <boolean>]
         [-alias <alias prefix for command interpreter>]
         [-file <file> [-format <format>]]
 
    load -readGroup <read group name>
         -sffDir <SFF directory>
         -regions <comma-separated region list>
         [-symLink <boolean>]
         [-filePrefix <SFF file prefix>]
         [-alias <alias prefix for command interpreter>]
         [-file <file> [-format <format>]]
 
    load -readGroup <read group name>
         -analysisDir <analysis directory>
         -regions <comma-separated region list>
         [-symLink <boolean>]
         [-filePrefix <SFF file prefix>]
         [-alias <alias prefix for command interpreter>]
         [-file <file> [-format <format>]]
 
    The 'load' command is used load read data into the currently open project.
    The different options combinations for running the 'load' command provide
    different ways of specifying what read data to load.
 
    For all forms of invocation, the read group into which the read data will
    be loaded must be provided using the '-readGroup' option.
 
    The '-symLink' option defaults to false, but may be specified as true.
    When specified as true, the read data files are not actually copied into
    the area of the disk that stores the Amplicon Project: a symbolic link
    to the data is created instead.
    
    The location of the read data files can be specified with either the
    '-sffDir' or '-analysisDir' options.  Use the '-sffDir' option to specify a
    directory that directly contains read data files (.sff files).  Use the
    '-analysisDir' option to specify an analysis directory.
 
    In addition to the location of the read data files, the specific read data
    to load must also be specified with the '-sffName' or '-regions' options.
    Use the '-sffName' option to specify the name of the SFF file to load.  Use
    the '-regions' option to specify the regions to load.  Regions must be
    specified in a comma separated list with no intervening spaces.  For
    example, '-regions 1,2,4', specifies that regions 1, 2, and 4 should be
    loaded.
 
    If the '-regions' option is used to specify the read data files to load,
    a '-filePrefix' option may be provided to restrict the loading to only
    those regions whose SFF file names begin with a certain prefix.  For
    example, in a given SFF directory there may be two region 1 files,
    TEST01.sff and REAL01.sff.  If you specify '-regions 1', both of these
    files will be loaded.  However, if you specify '-regions 1 -filePrefix
    REAL', only the later file will be loaded.
 
    An alias may be provided that allows loaded read data to be referenced by
    subsequent commands.  For example, if we run
    'load -readGroup MyGroup -sffDir some/path/sff -regions 1,2 -alias read',
    we can subsequently refer to the imported region read data as "read01" and
    "read02".  For example, we can run:
         'assoc -readData read01 -sample sample1 -amplicon amplicon1'
    (assuming sample1 and amplicon1 exist).  The alias is constructed by taking
    the value passed to the '-alias' option and appending two digits specifying
    the region.  This option facilitates the creation of scripts that load from
    analysis directories, wherein the regions of interest are known in
    advance, but the actual SFF file names are not known (since they are 
    automatically given names by the pipeline software).
 
    Here are some examples of valid 'load' invocations.
 
    load -readGroup Group1 -sffDir /data/sff -sffName TEST01.sff
 
        This will load the read data in /data/sff/TEST01.sff into the read
        group named "Group1" of the currently open project.
 
    load -readGroup Group1 -analysisDir /data/analysis1 \
                           -regions 1,2,4 -alias Read
 
        This will load the read data of regions 1, 2, and 4 inside the analysis
        directory /data/analysis1 into the read group named "Group1" of the
        currently open project.  Subsequent commands will be able to refer to
        the read data as "Read01", "Read02", and "Read04".
 
    load -readGroup Group1 -analysisDir /data/analysis1 \
                           -regions 2 -filePrefix TEST -alias Read
 
        This will load the read data of region 2 inside the analysis directory
        /data/analysis1 into the read group named "Group1" of the currently
        open project.  Only SFF files with prefix "TEST" in the analysis will
        be considered.
 
    Run 'help general tabularCommands' for information about the '-file'
    option.
    
    Run 'help general filePaths' for more information about the interpretation
    of relative paths when using the '-file', '-analysisDir' or '-sffDir' 
    options.