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FastQValidator (view source)

Revision as of 14:16, 22 February 2010

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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 ==
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'''Required Parameters:'''
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        --file  :  FastQ filename with path to be prorcessed.
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'''Optional Parameters:'''
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        --minReadLen        : Minimum allowed read length (Defaults to 10).
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        --maxReportedErrors : Maximum number of errors to display before suppressing them (Defaults to 20).
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        --ignoreAllErrors  : Ignore all errors (same as --maxReportedErrors 0), overwrites the maxReportedErrors option.
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'''Optional Space Options for Raw Sequence (Last one specified is used):'''
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        --autoDetect : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default).
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        --baseSpace  : ACTGN only
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        --colorSpace : 0123. only
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'''Usage:'''
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        ./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--maxReportedErrors <maxReprotedErrors>|--ignoreAllErrors] [--baseSpace|--colorSpace|--autoDetect]
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'''Examples:'''
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        ../fastQValidator --file testFile.txt
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        ../fastQValidator --file testFile.txt --minReadLen 10 --baseSpace --maxReportedErrors 100
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        ./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreAllErrors
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== FastQ Validator Output ==
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When running the fastQValidator Executable, the output starts with a summary of the parameters:
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The following parameters are in effect:
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Input Parameters
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--file [testFile.txt], --minReadLen [10]
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  Space Type : --baseSpace [ON], --colorSpace, --autoDetect
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      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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For Example:
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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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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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== 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 ==
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'''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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== FastQ Validator Output ==
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When running the fastQValidator Executable, the output starts with a summary of the parameters:
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The following parameters are in effect:
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              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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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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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.
 
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/518"

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