def mainRun():
    '''
    This is the primary function for external typical users to run when the Command Line Interface is used
    '''
    #start up the logger
    initLogger()
    
    #attempt to parse the arguments
    p = ap.ArgumentParser(description=util.DESC, formatter_class=ap.RawTextHelpFormatter)
    
    #version data
    p.add_argument('-V', '--version', action='version', version='%(prog)s' + \
                   ' %s in MSBWT %s' % (util.VERSION, util.PKG_VERSION))
    
    #TODO: do we want subparsers groups by type or sorted by name? it's type currently
    
    sp = p.add_subparsers(dest='subparserID')
    p2 = sp.add_parser('cffq', help='create a MSBWT from FASTQ files (pp + cfpp)')
    p2.add_argument('-p', metavar='numProcesses', dest='numProcesses', type=int, default=1, help='number of processes to run (default: 1)')
    p2.add_argument('-u', '--uniform', dest='areUniform', action='store_true', help='the input sequences have uniform length', default=False)
    p2.add_argument('-c', '--compressed', dest='buildCompressed', action='store_true', help='build the RLE BWT (faster, less disk I/O)', default=False)
    p2.add_argument('outBwtDir', type=util.newDirectory, help='the output MSBWT directory')
    p2.add_argument('inputFastqs', nargs='+', type=util.readableFastqFile, help='the input FASTQ files')
    
    p7 = sp.add_parser('pp', help='pre-process FASTQ files before BWT creation')
    p7.add_argument('-u', '--uniform', dest='areUniform', action='store_true', help='the input sequences have uniform length', default=False)
    p7.add_argument('outBwtDir', type=util.newDirectory, help='the output MSBWT directory')
    p7.add_argument('inputFastqs', nargs='+', type=util.readableFastqFile, help='the input FASTQ files')
    
    p3 = sp.add_parser('cfpp', help='create a MSBWT from pre-processed sequences and offsets')
    p3.add_argument('-p', metavar='numProcesses', dest='numProcesses', type=int, default=1, help='number of processes to run (default: 1)')
    p3.add_argument('-u', '--uniform', dest='areUniform', action='store_true', help='the input sequences have uniform length', default=False)
    p3.add_argument('-c', '--compressed', dest='buildCompressed', action='store_true', help='build the RLE BWT (faster, less disk I/O)', default=False)
    p3.add_argument('bwtDir', type=util.existingDirectory, help='the MSBWT directory to process')
    
    p4 = sp.add_parser('merge', help='merge many MSBWTs into a single MSBWT')
    p4.add_argument('-p', metavar='numProcesses', dest='numProcesses', type=int, default=1, help='number of processes to run (default: 1)')
    p4.add_argument('outBwtDir', type=util.newDirectory, help='the output MSBWT directory')
    p4.add_argument('inputBwtDirs', nargs='+', type=util.existingDirectory, help='input BWT directories to merge')
    
    p5 = sp.add_parser('query', help='search for a sequence in an MSBWT, prints sequence and seqID')
    p5.add_argument('inputBwtDir', type=util.existingDirectory, help='the BWT to query')
    p5.add_argument('kmer', type=util.validKmer, help='the input k-mer to search for')
    p5.add_argument('-d', '--dump-seqs', dest='dumpSeqs', action='store_true', help='print all sequences with the given kmer (default=False)', default=False)
    
    p6 = sp.add_parser('massquery', help='search for many sequences in an MSBWT')
    p6.add_argument('inputBwtDir', type=util.existingDirectory, help='the BWT to query')
    p6.add_argument('kmerFile', help='a file with one k-mer per line')
    p6.add_argument('outputFile', help='output file with counts per line')
    p6.add_argument('-r', '--rev-comp', dest='reverseComplement', action='store_true', help='also search for each kmer\'s reverse complement', default=False)
    
    p8 = sp.add_parser('compress', help='compress a MSBWT from byte/base to RLE')
    p8.add_argument('-p', metavar='numProcesses', dest='numProcesses', type=int, default=1, help='number of processes to run (default: 1)')
    p8.add_argument('srcDir', type=util.existingDirectory, help='the source directory for the BWT to compress')
    p8.add_argument('dstDir', type=util.newDirectory, help='the destination directory')
    
    p9 = sp.add_parser('decompress', help='decompress a MSBWT from RLE to byte/base')
    p9.add_argument('-p', metavar='numProcesses', dest='numProcesses', type=int, default=1, help='number of processes to run (default: 1)')
    p9.add_argument('srcDir', type=util.existingDirectory, help='the source directory for the BWT to compress')
    p9.add_argument('dstDir', type=util.newDirectory, help='the destination directory')
    
    p10 = sp.add_parser('convert', help='convert from a raw text input to RLE')
    p10.add_argument('-i', metavar='inputTextFN', dest='inputTextFN', default=None, help='input text filename (default: stdin)')
    p10.add_argument('dstDir', type=util.newDirectory, help='the destination directory')
    
    args = p.parse_args()
    
    if args.subparserID == 'cffq':
        logger.info('Inputs:\t'+str(args.inputFastqs))
        logger.info('Uniform:\t'+str(args.areUniform))
        logger.info('Output:\t'+args.outBwtDir)
        logger.info('Output Compressed:\t'+str(args.buildCompressed))
        logger.info('Processes:\t'+str(args.numProcesses))
        if args.numProcesses > 1:
            logger.warning('Using multi-processing with slow disk accesses can lead to slower build times.')
        print
        if args.areUniform:
            #if they are uniform, use the method developed by Bauer et al., it's likely short Illumina seq
            if args.buildCompressed:
                MultiStringBWT.createMSBWTCompFromFastq(args.inputFastqs, args.outBwtDir, args.numProcesses, args.areUniform, logger)
            else:
                MultiStringBWT.createMSBWTFromFastq(args.inputFastqs, args.outBwtDir, args.numProcesses, args.areUniform, logger)
        else:
            #if they aren't uniform, use the merge method by Holt et al., it's likely longer PacBio seq
            if args.buildCompressed:
                logger.error('No compressed builder for non-uniform datasets, compress after creation.')
            else:
                Multimerge.createMSBWTFromFastq(args.inputFastqs, args.outBwtDir, args.numProcesses, args.areUniform, logger)
        
    elif args.subparserID == 'pp':
        logger.info('Inputs:\t'+str(args.inputFastqs))
        logger.info('Uniform:\t'+str(args.areUniform))
        logger.info('Output:\t'+args.outBwtDir)
        if args.areUniform:
            #preprocess for Bauer et al. method
            MultiStringBWT.preprocessFastqs(args.inputFastqs, args.outBwtDir, args.areUniform, logger)
        else:
            #preprocess for Holt et al. method
            numProcs = 1
            Multimerge.preprocessFastqs(args.inputFastqs, args.outBwtDir, numProcs, args.areUniform, logger)
        
    elif args.subparserID == 'cfpp':
        logger.info('BWT dir:\t'+args.bwtDir)
        logger.info('Uniform:\t'+str(args.areUniform))
        logger.info('Output Compressed:\t'+str(args.buildCompressed))
        logger.info('Processes:\t'+str(args.numProcesses))
        if args.numProcesses > 1:
            logger.warning('Using multi-processing with slow disk accesses can lead to slower build times.')
        print
        seqFN = args.bwtDir+'/seqs.npy'
        offsetFN = args.bwtDir+'/offsets.npy'
        bwtFN = args.bwtDir+'/msbwt.npy'
        
        if args.areUniform:
            #process it using the column-wise Bauer et al. method
            if args.buildCompressed:
                MSBWTCompGenCython.createMsbwtFromSeqs(args.bwtDir, args.numProcesses, logger)
            else:
                MSBWTGenCython.createMsbwtFromSeqs(args.bwtDir, args.numProcesses, logger)
        else:
            #process it using the Holt et al. merge method
            if args.buildCompressed:
                logger.error('No compressed builder for non-uniform datasets, compress after creation.')
            else:
                Multimerge.interleaveLevelMerge(args.bwtDir, args.numProcesses, args.areUniform, logger)
        
    elif args.subparserID == 'compress':
        logger.info('Source Directory:'+args.srcDir)
        logger.info('Dest Directory:'+args.dstDir)
        logger.info('Processes:'+str(args.numProcesses))
        if args.srcDir == args.dstDir:
            raise Exception('Source and destination directories cannot be the same directory.')
        print
        MSBWTGen.compressBWT(args.srcDir+'/msbwt.npy', args.dstDir+'/comp_msbwt.npy', args.numProcesses, logger)
        
    elif args.subparserID == 'decompress':
        logger.info('Source Directory: '+args.srcDir)
        logger.info('Dest Directory: '+args.dstDir)
        logger.info('Processes: '+str(args.numProcesses))
        print
        MSBWTGen.decompressBWT(args.srcDir, args.dstDir, args.numProcesses, logger)
        #TODO: remove if srcdir and dstdir are the same?
        
    elif args.subparserID == 'merge':
        logger.info('Inputs:\t'+str(args.inputBwtDirs))
        logger.info('Output:\t'+args.outBwtDir)
        logger.info('Processes:\t'+str(args.numProcesses))
        if args.numProcesses > 1:
            logger.warning('Multi-processing is not supported at this time, but will be included in a future release.')
            numProcs = 1
            #logger.warning('Using multi-processing with slow disk accesses can lead to slower build times.')
        print
        #MSBWTGen.mergeNewMSBWT(args.outBwtDir, args.inputBwtDirs, args.numProcesses, logger)
        if len(args.inputBwtDirs) > 2:
            #this is a deprecated method, it may still work if you feel daring
            #MSBWTGenCython.mergeMsbwts(args.inputBwtDirs, args.outBwtDir, 1, logger)
            logger.error('Merging more than two MSBWTs at once is not currently supported.')
        else:
            GenericMerge.mergeTwoMSBWTs(args.inputBwtDirs[0], args.inputBwtDirs[1], args.outBwtDir, numProcs, logger)
        
    elif args.subparserID == 'query':
        #this is the easiest thing we can do, don't dump the standard info, just do it
        msbwt = MultiStringBWT.loadBWT(args.inputBwtDir, logger=logger)
        
        #always print how many are found, users can parse it out if they want
        r = msbwt.findIndicesOfStr(args.kmer)
        print r[1]-r[0]
        
        #dump the seqs if request
        if args.dumpSeqs:
            for x in xrange(r[0], r[1]):
                dInd = msbwt.getSequenceDollarID(x)
                print msbwt.recoverString(dInd)[1:]+','+str(dInd)
    
    elif args.subparserID == 'massquery':
        logger.info('Input:\t'+str(args.inputBwtDir))
        logger.info('Queries:\t'+str(args.kmerFile))
        logger.info('Output:\t'+args.outputFile)
        logger.info('Rev-comp:\t'+str(args.reverseComplement))
        print
        msbwt = MultiStringBWT.loadBWT(args.inputBwtDir, logger=logger)
        
        output = open(args.outputFile, 'w+')
        output.write('k-mer,counts')
        if args.reverseComplement:
            output.write(',revCompCounts\n')
        else:
            output.write('\n')
        
        logger.info('Beginning queries...')
        for line in open(args.kmerFile, 'r'):
            kmer = line.strip('\n')
            c = msbwt.countOccurrencesOfSeq(kmer)
            if args.reverseComplement:
                rc = msbwt.countOccurrencesOfSeq(MultiStringBWT.reverseComplement(kmer))
                output.write(kmer+','+str(c)+','+str(rc)+'\n')
            else:
                output.write(kmer+','+str(c)+'\n')
        logger.info('Queries complete.')
    
    elif args.subparserID == 'convert':
        if args.inputTextFN == None:
            logger.info('Input: stdin')
        else:
            logger.info('Input: '+args.inputTextFN)
        logger.info('Output: '+args.dstDir)
        logger.info('Beginning conversion...')
        CompressToRLE.compressInput(args.inputTextFN, args.dstDir)
        logger.info('Finished conversion.')
        
    else:
        print args.subparserID+" is currently not implemented, please wait for a future release."