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| == How to Use the fastQValidator Executable == | | == How to Use the fastQValidator Executable == |
− | '''Required Parameters:'''
| + | === Required Parameters === |
| --file : FastQ filename with path to be prorcessed. | | --file : FastQ filename with path to be prorcessed. |
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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
| + | --quitAfterErrorNum : 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 | | --maxReportedErrors : Maximum number of errors to display before |
| suppressing them (Defaults to 20). | | suppressing them (Defaults to 20). |
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| Base Composition printing if printBaseComp is set. | | Base Composition printing if printBaseComp is set. |
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− | '''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). | | --autoDetect : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default). |
| --baseSpace : ACTGN only | | --baseSpace : ACTGN only |
| --colorSpace : 0123. only | | --colorSpace : 0123. only |
| | | |
− | '''Usage:'''
| + | === Usage === |
| ./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--quitAfterErrorNum] [--maxReportedErrors <maxReprotedErrors>|--ignoreAllErrors] [--baseSpace|--colorSpace|--autoDetect] [--printBaseComp] [--disableAllMessages] | | ./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--quitAfterErrorNum] [--maxReportedErrors <maxReprotedErrors>|--ignoreAllErrors] [--baseSpace|--colorSpace|--autoDetect] [--printBaseComp] [--disableAllMessages] |
| | | |
− | '''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 --maxReportedErrors 100 |
| ./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreAllErrors | | ./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreAllErrors |
| + | |
| + | === Return Value === |
| + | * 0 - the fastq file is valid. |
| + | * < 0 - invalid options specified. |
| + | * > 0 - fastq file did not validate succesfully. One of the [[C++ Class: FastQFile#Public Class Enums|FastQStatus]] failure values is returned |
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| Errors : --ignoreAllErrors, --maxReportedErrors [100] | | Errors : --ignoreAllErrors, --maxReportedErrors [100] |
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− | The Validator Executable outputs error messages for invalid sequences based on [[FastQFile#Validation Criteria Used For Reading a Sequence|Validation Criteria]]. | + | 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: |
− | For Example: | |
| ERROR on Line 25: The sequence identifier line was too short. | | 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 29: First line of a sequence does not begin wtih @ |
| ERROR on Line 33: No Sequence Identifier specified before the comment. | | ERROR on Line 33: No Sequence Identifier specified before the comment. |
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− | Base Composition Percentages by Index: | + | Base Composition Percentages by Index are printed if --printBaseComp is set to ON. For Example: |
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| Base Composition Statistics: | | Base Composition Statistics: |
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| Finished processing testFile.txt with 92 lines containing 20 sequences. | | Finished processing testFile.txt with 92 lines containing 20 sequences. |
| There were a total of 17 errors. | | There were a total of 17 errors. |
− |
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− | The fastQValidator returns 0 on success and non-zero on failure.
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| == Libraries & Classes == | | == Libraries & Classes == |
− | *[[FastQFile#Libraries & Classes|libfqf.a]] | + | *[[C++ Library: libfqf|libfqf.a]] |
| *FastQValidator.cpp - Main method for the Executable. | | *FastQValidator.cpp - Main method for the Executable. |
− | *libcsg.a | + | *[[C++ Library: libcsg|libcsg.a]] |
| **ParameterList - Class for reading in Parameters. | | **ParameterList - Class for reading in Parameters. |
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