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FastQValidator (view source)

Revision as of 13:52, 22 February 2010

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== Status  ==
 
== Status  ==
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The [http://en.wikipedia.org/wiki/FASTQ_format FastQ] Validator is on our [[Todo List]].  
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The initial version of a [http://en.wikipedia.org/wiki/FASTQ_format FastQ] Validator is complete.  
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An initial version of the [[FastQFile]] has been completed which includes validation methods.
      
== Valid FastQ File Requirements  ==
 
== Valid FastQ File Requirements  ==
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A valid fastQ file should meet the following requirements:
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A valid fastQ file meets the validation criteria specified in [[FastQFile]].
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*A base sequence should have non-zero length.
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*A quality string should be present for every base sequence.
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== Additional Features ==
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*Paired quality and base sequences should be of the same length.
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*Base composition reported and tracked by position.
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*Supports base space and color space files.
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*Consumes gzipped and uncompressed text files transparently.
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*Prints error messages for errors up to the configurable maximum number of reportable errors.
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*Prints a summary of the total number of errors.
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*Prints the total number of lines processed as well as the total number of sequences processed.  
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*Valid quality values should all have ASCII codes > 32.
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*Valid bases should be ACTG or N, unless ambiguous bases are explicitly allowed by the application consuming the file. Lower case characters are allowed.
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== Additional Wishlist - Not Implemented ==
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*Every entry in the file should have a unique identifier.
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There are a series of optional capabilities a FastQ Validator could implement. Among those:  
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*Reads should be of a minimum length; many mappers will get into trouble with very short reads.
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*Base composition should be reported and tracked by position.
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== Additional Wishlist  ==
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There are a series of optional capabilities a FastQ Validator should implement. Among those:  
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*Consume gzipped and uncompressed text files transparently (see libcsg/InputFile.h).
      
*To reduce memory usage, implement a two-pass algorithm that stores only a key for each sequence name (rather than complete sequence names) in memory (suggest a pair of options -1 -> one pass, high memory use, -2 -> two pass lower memory use, default is -1).
 
*To reduce memory usage, implement a two-pass algorithm that stores only a key for each sequence name (rather than complete sequence names) in memory (suggest a pair of options -1 -> one pass, high memory use, -2 -> two pass lower memory use, default is -1).
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*Support color space files, where valid base sequences include the characters 0, 1, 2, 3, '.' (period) in addition to A, C, T, G and N (some csfastq sequence lines start with a primer base).
      
== Discussion ==
 
== Discussion ==
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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/512"

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