Changes

'''Optional Parameters:'''

'''Optional Parameters:'''

         --minReadLen       : Minimum allowed read length (Defaults to 10).

         --minReadLen         : Minimum allowed read length (Defaults to 10).

         --maxReportedErrors : Maximum number of errors to display before suppressing them (Defaults to 20).

         --maxReportedErrors : Maximum number of errors to display before

         --ignoreAllErrors   : Ignore all errors (same as --maxReportedErrors 0), overwrites the maxReportedErrors option.

                              suppressing them (Defaults to 20).

--printBaseComp      : turns on the printing of Base Composition Statistics.

         --ignoreAllErrors   : Ignore all errors (same as maxReportedErrors = 0)

--disableAllMessages : turns off all prints, including errors, and summary

                              overwrites the maxReportedErrors option.

                      statistics (Defaults to enabled).  Does not turn off

        --printBaseComp      : turns on the printing of Base Composition Statistics.

                      Base Composition printing if printBaseComp is set.

        --disableAllMessages : turns off all prints, including errors, and summary

                              statistics (Defaults to enabled).  Does not turn off

                              Base Composition printing if printBaseComp is set.

'''Optional Space Options for Raw Sequence (Last one specified is used):'''

'''Optional Space Options for Raw Sequence (Last one specified is used):'''