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| A valid fastQ file meets the validation criteria specified in [[FastQFile#Validation Criteria Used For Reading a Sequence|FastQ File Validation]]. | | A valid fastQ file meets the validation criteria specified in [[FastQFile#Validation Criteria Used For Reading a Sequence|FastQ File Validation]]. |
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| + | |
| + | == How to Use the fastQValidator Executable == |
| + | '''Required Parameters:''' |
| + | --file : FastQ filename with path to be prorcessed. |
| + | |
| + | '''Optional Parameters:''' |
| + | --minReadLen : Minimum allowed read length (Defaults to 10). |
| + | --maxReportedErrors : Maximum number of errors to display before suppressing them (Defaults to 20). |
| + | --ignoreAllErrors : Ignore all errors (same as --maxReportedErrors 0), overwrites the maxReportedErrors option. |
| + | |
| + | '''Optional Space Options for Raw Sequence (Last one specified is used):''' |
| + | --autoDetect : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default). |
| + | --baseSpace : ACTGN only |
| + | --colorSpace : 0123. only |
| + | |
| + | '''Usage:''' |
| + | ./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--maxReportedErrors <maxReprotedErrors>|--ignoreAllErrors] [--baseSpace|--colorSpace|--autoDetect] |
| + | |
| + | '''Examples:''' |
| + | ../fastQValidator --file testFile.txt |
| + | ../fastQValidator --file testFile.txt --minReadLen 10 --baseSpace --maxReportedErrors 100 |
| + | ./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreAllErrors |
| + | |
| + | |
| + | == FastQ Validator Output == |
| + | When running the fastQValidator Executable, the output starts with a summary of the parameters: |
| + | |
| + | The following parameters are in effect: |
| + | |
| + | Input Parameters |
| + | --file [testFile.txt], --minReadLen [10] |
| + | Space Type : --baseSpace [ON], --colorSpace, --autoDetect |
| + | Errors : --ignoreAllErrors, --maxReportedErrors [100] |
| + | |
| + | The Validator Executable outputs error messages for invalid sequences based on [[FastQFile#Validation Criteria Used For Reading a Sequence|Validation Criteria]]. |
| + | For Example: |
| + | ERROR on Line 25: The sequence identifier line was too short. |
| + | ERROR on Line 29: First line of a sequence does not begin wtih @ |
| + | ERROR on Line 33: No Sequence Identifier specified before the comment. |
| + | |
| + | Base Composition Percentages by Index: |
| + | |
| + | Base Composition Statistics: |
| + | Read Index %A %C %G %T %N Total Reads At Index |
| + | 0 100.00 0.00 0.00 0.00 0.00 20 |
| + | 1 5.00 95.00 0.00 0.00 0.00 20 |
| + | 2 5.00 0.00 5.00 90.00 0.00 20 |
| + | |
| + | |
| + | Summary of the number of lines, sequences, and errors: |
| + | Finished processing testFile.txt with 92 lines containing 20 sequences. |
| + | There were a total of 17 errors. |
| + | |
| | | |
| == Additional Features == | | == Additional Features == |
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| * It may be useful to report 2 types of information to the user: ERROR (critical failure) and WARNING (tolerable errors). | | * It may be useful to report 2 types of information to the user: ERROR (critical failure) and WARNING (tolerable errors). |
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− | == How to Use the fastQValidator Executable ==
| |
− | '''Required Parameters:'''
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− | -f : FastQ filename with path to be prorcessed.
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− |
| |
− | '''Optional Parameters:'''
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− | -l : Minimum allowed read length (Defaults to 10).
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− | -e : Maximum number of errors to display before suppressing them(Defaults to 20).
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− | -b : Raw sequence type: "A"/"C"/"G"/"T"/"N" - Bases only;
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− | "0"/"1"/"2"/"3"/"." - Color space only;
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− | "" - Base Decision on the first Raw Sequence Character (Default)
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− | All other characters - Bases & Color space
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− |
| |
− | '''Testing only Parameters:'''
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− | -t : If "ReadOnly" is specified, the fastq will be read but not processed. This may be used for determining read time.
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− | '''Usage:'''
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− | ./fastQValidator -f <fileName> -l <minReadLen> -e <maxReprotedErrors> -b <rawSeqType>
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− |
| |
− | '''Examples:'''
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− | ../fastQValidator -f testFile.txt
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− | ../fastQValidator -f testFile.txt -l 10 -b A -e 100
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− | ./fastQValidator -f test/testFile.txt -l 10 -b Z -e 100
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− | time ./fastQValidator -f test/testFile.txt -t ReadOnly
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− |
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− |
| |
− | == FastQ Validator Output ==
| |
− | When running the fastQValidator Executable, the output starts with a summary of the parameters:
| |
− | The following parameters are in effect:
| |
− | FastQ File Name : testFile.txt (-fname)
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− | Min Read Length : 10 (-l9999)
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− | Max Reported Errors : 100 (-e9999)
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− | BaseType : A (-bname)
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− | TestMode : (-tname)
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− |
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− | Both the Executable and the Library outputs the following:
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− | *Error messages for the first Configurable number of errors.:
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− | ERROR on Line 25: The sequence identifier line was too short.
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− | ERROR on Line 29: First line of a sequence does not begin wtih @
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− | ERROR on Line 33: No Sequence Identifier specified before the comment.
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− | *Base Composition Percentages by Index:
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− |
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− | Base Composition Statistics:
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− | Read Index %A %C %G %T %N Total Reads At Index
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− | 0 100.00 0.00 0.00 0.00 0.00 20
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− | 1 5.00 95.00 0.00 0.00 0.00 20
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− | 2 5.00 0.00 5.00 90.00 0.00 20
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− | *Summary of the number of lines, sequences, and errors:
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− | Finished processing testFile.txt with 92 lines containing 20 sequences.
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− | There were a total of 17 errors.
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