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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 == | | == 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). |
− | -b : Raw sequence type: B - ACTGN only (Default) | + | -b : Raw sequence type: "A"/"C"/"G"/"T"/"N" - Bases only; |
− | C - 0123. only
| + | "0"/"1"/"2"/"3"/"." - Color space only; |
− | BC - ACTGN or 0123. | + | "" - Base Decision on the first Raw Sequence Character (Default) |
| + | 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 |
− | ../fastQValidator -f testFile.txt -l 10 -b BC -e 100 | + | ../fastQValidator -f testFile.txt -l 10 -b A -e 100 |
− | ./fastQValidator -f test/testFile.txt -l 10 -b BC -e 100 | + | ./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 |
− |
| |
− |
| |
− | == 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.
| |
| | | |
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| Min Read Length : 10 (-l9999) | | Min Read Length : 10 (-l9999) |
| Max Reported Errors : 100 (-e9999) | | Max Reported Errors : 100 (-e9999) |
− | BaseType : BC (-bname) | + | BaseType : A (-bname) |
| TestMode : (-tname) | | TestMode : (-tname) |
| | | |