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| === 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) | + | Different than maxErrors since |
− | overwrites the maxReportedErrors option. | + | printableErrors will continue reading and |
− | --printBaseComp : turns on the printing of Base Composition Statistics. | + | validating the file until the end, but |
− | --disableAllMessages : turns off all prints, including errors, and summary
| + | just doesn't print the errors. |
− | 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 === |
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| | | |
| 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: |