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LibStatGen: FASTQ (view source)

Revision as of 12:37, 19 February 2010

1,622 bytes added ,  12:37, 19 February 2010
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== How to Use the fastQFile Library ==
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*'''Library Name:''' libfqf.a
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*'''Include Files:''' FastQFile.h, StringBasics.h (for String parameter)
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*'''Class Name:''' FastQFile
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** Constructor Parameters:
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*** int minReadLength - The minimum length that a base sequence must be for it to be valid.
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*** int maxReportedErrors - The maximum number of errors that should be reported in detail before suppressing the errors.
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*'''Open a FastQ File:''' openFile
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** Parameters:
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*** String filename - fastq file to be opened.
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*** String baseType- Raw sequence type enter:
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****  "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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** Return Value
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*** FastQStatus: FASTQ_SUCCESS if successfully opened, FASTQ_FAILURE if not.
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*'''Close a FastQ File:''' closeFile
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** Parameters: NONE
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** Return Value
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*** bool: FastQStatus - FASTQ_SUCCESS if successfully closed, FASTQ_FAILURE if not.
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*'''Determine if a FastQ File is open Method:''' isOpen
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** Parameters: NONE
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** Return Value
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*** bool: true if a file is open, false if not.
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*'''Validate a FastQ File:''' validateFastQFile
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** Parameters:
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*** String filename - fastq file to be validated.
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*** String baseType- Raw sequence type enter:
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****  "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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** Return Value
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*** bool: true if there were no errors in the file, false otherwise.
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*'''Read a FastQ Sequence From the File:''' readFastQSequence
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** Parameters: NONE
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** Return Value
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*** int: FASTQ_SUCCESS if successfully read and valid, FASTQ_FAILURE if not successfully read, FASTQ_INVALID if the sequence was invalid..
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*'''Get the Space Type for the File:''' getSpaceType
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** Parameters: NONE
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** Return Value
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*** BaseAsciiMap::SPACETYPE: COLOR_SPACE if the file is color space (0,1,2,3,.), BASE_SPACE if the file is base space (A,C,G,T,N), BOTH_SPACE if the file is both (0,1,2,3,.,A,C,G,T,N), or UNKNOWN if it has yet to be determined.
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== Validation Criteria ==
 
== Validation Criteria ==
 
{| class="wikitable" style="width:100%" border="1"
 
{| class="wikitable" style="width:100%" border="1"
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         -l  :  Minimum allowed read length (Defaults to 10).
 
         -l  :  Minimum allowed read length (Defaults to 10).
 
         -e  :  Maximum number of errors to display before suppressing them(Defaults to 20).
 
         -e  :  Maximum number of errors to display before suppressing them(Defaults to 20).
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         -b  :  Raw sequence type:  B - ACTGN only (Default)
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         -b  :  Raw sequence type: "A"/"C"/"G"/"T"/"N"  - Bases only;
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                                  C - 0123. only
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                                  "0"/"1"/"2"/"3"/"." - Color space only;
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                                   BC - ACTGN or 0123.
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                                  ""                  - Base Decision on the first Raw Sequence Character (Default)
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                                   All other characters - Bases & Color space
    
'''Testing only Parameters:'''
 
'''Testing only Parameters:'''
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'''Examples:'''
 
'''Examples:'''
 
         ../fastQValidator -f testFile.txt
 
         ../fastQValidator -f testFile.txt
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         ../fastQValidator -f testFile.txt -l 10 -b BC -e 100
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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 BC -e 100
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         ./fastQValidator -f test/testFile.txt -l 10 -b Z -e 100
 
         time ./fastQValidator -f test/testFile.txt -t ReadOnly
 
         time ./fastQValidator -f test/testFile.txt -t ReadOnly
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  −
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== How to Use the fastQValidator Library ==
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*'''Library Name:''' libfqv.a
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*'''Include Files:''' FastQValidator.h, StringBasics.h (for String parameter)
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*'''Class Name:''' FastQValidator
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** Constructor Parameters:
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*** int minReadLength - The minimum length that a base sequence must be for it to be valid.
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*** int maxReportedErrors - The maximum number of errors that should be reported in detail before suppressing the errors.
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*** String baseType- Raw sequence type:
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****  "B" - Bases only;
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****  "C" - Color space only;
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**** "BC" - Bases & Color space
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*'''Validation Method:''' validateFastQFile
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** Parameters:
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*** String filename - fastq file to be validated.
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** Return Value
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*** bool: true if there were no errors in the file, false otherwise.
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               Min Read Length :              10 (-l9999)
 
               Min Read Length :              10 (-l9999)
 
           Max Reported Errors :            100 (-e9999)
 
           Max Reported Errors :            100 (-e9999)
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                       BaseType :             BC (-bname)
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                       BaseType :               A (-bname)
 
                       TestMode :                (-tname)
 
                       TestMode :                (-tname)
  
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/498"

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