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FastQValidator (view source)

Revision as of 10:42, 7 April 2010

290 bytes added ,  10:42, 7 April 2010
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== How to Use the fastQValidator Executable ==
 
== How to Use the fastQValidator Executable ==
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'''Required Parameters:'''
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=== Required Parameters ===
 
         --file  :  FastQ filename with path to be prorcessed.
 
         --file  :  FastQ filename with path to be prorcessed.
   −
'''Optional Parameters:'''
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=== Optional Parameters ===
 
         --minReadLen        : Minimum allowed read length (Defaults to 10).
 
         --minReadLen        : Minimum allowed read length (Defaults to 10).
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--quitAfterErrorNum  : Number of errors to allow before quitting
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        --quitAfterErrorNum  : Number of errors to allow before quitting
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                      reading/validating the file.
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                              reading/validating the file.
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                      -1 (default) indicates to not quit until
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                              -1 (default) indicates to not quit until
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                      the entire file is read.
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                              the entire file is read.
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                      0 indicates not to read/validate anything
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                              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):'''
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=== 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
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'''Usage:'''
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=== 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]
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'''Examples:'''
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=== 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
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=== Return Value ===
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* 0 - the fastq file is valid.
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* < 0 - invalid options specified.
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* > 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]].
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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:
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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.
   −
Base Composition Percentages by Index:
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Base Composition Percentages by Index are printed if --printBaseComp is set to ON.  For Example:
    
  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.
         
== Libraries & Classes ==
 
== Libraries & Classes ==
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*[[FastQFile#Libraries & Classes|libfqf.a]]
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*[[C++ Library: libfqf|libfqf.a]]
 
*FastQValidator.cpp - Main method for the Executable.
 
*FastQValidator.cpp - Main method for the Executable.
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*libcsg.a
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*[[C++ Library: libcsg|libcsg.a]]
 
**ParameterList - Class for reading in Parameters.
 
**ParameterList - Class for reading in Parameters.
  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/979"

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