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LibStatGen: FASTQ

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

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