Changes

=== Optional Parameters ===

=== Optional Parameters ===

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

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

         --quitAfterErrorNum  : Number of errors to allow before quitting

         --maxErrors          : Number of errors to allow before quitting

                               reading/validating the file.

                               reading/validating the file.

                               -1 (default) indicates to not quit until

                               -1 (default) indicates to not quit until

                               the entire file is read.

                               the entire file is read.

                               0 indicates not to read/validate anything

                               0 indicates not to read/validate anything

         --maxReportedErrors  : Maximum number of errors to display before

         --printableErrors    : Maximum number of errors to print before

                               suppressing them (Defaults to 20).

                               suppressing them (Defaults to 20).

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

                               overwrites the maxReportedErrors option.

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

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

                              statistics (Defaults to enabled). Does not turn off

         --ignoreErrors      : Ignore all errors (same as printableErrors = 0)

                              Base Composition printing if printBaseComp is set.

                               overwrites the printableErrors option.

         --baseComposition    : Print the Base Composition Statistics.

--quiet              : Suppresses the display of errors and summary statistics.

                      Does not affect the printing of Base Composition Statistics.

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

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

         --autoDetect : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default).

         --auto      : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default).

         --baseSpace  : ACTGN only

         --baseSpace  : ACTGN only

         --colorSpace : 0123. only (with 1 character primer base)

         --colorSpace : 0123. only (with 1 character primer base)

=== Usage ===

=== Usage ===

         ./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--quitAfterErrorNum] [--maxReportedErrors <maxReprotedErrors>|--ignoreAllErrors] [--baseSpace|--colorSpace|--autoDetect] [--printBaseComp] [--disableAllMessages]

         ./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--maxErrors <numErrors>] [--printableErrors <printableErrors>|--ignoreErrors] [--baseSpace|--colorSpace|--auto] [--baseComposition] [--quiet]

=== Examples ===

=== Examples ===

         ./fastQValidator --file testFile.txt

         ./fastQValidator --file testFile.txt

         ./fastQValidator --file testFile.txt --minReadLen 10 --baseSpace --maxReportedErrors 100

         ./fastQValidator --file testFile.txt --minReadLen 10 --baseSpace --printableErrors 100

         ./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreAllErrors

         ./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreErrors

=== Return Value ===

=== Return Value ===

  Input Parameters

  Input Parameters

  --file [testFile.txt], --printBaseComp [ON], --disableAllMessages, --minReadLen [10],

  --file [testFile.txt], --baseComposition [ON], --quiet, --minReadLen [10],

                 --quitAfterErrorNum [-1]

                 --maxErrors [-1]

   Space Type : --baseSpace [ON], --colorSpace, --autoDetect

   Space Type : --baseSpace [ON], --colorSpace, --auto

       Errors : --ignoreAllErrors, --maxReportedErrors [100]

       Errors : --ignoreErrors, --printableErrors [100]

The Validator Executable outputs error messages for invalid sequences based on [[C++ Class: FastQFile#Validation Criteria Used For Reading a Sequence|Validation Criteria]].  For Example:

The Validator Executable outputs error messages for invalid sequences based on [[C++ Class: FastQFile#Validation Criteria Used For Reading a Sequence|Validation Criteria]].  For Example: