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LibStatGen: FASTQ (view source)

Revision as of 10:49, 2 February 2017

54 bytes added ,  10:49, 2 February 2017
→‎Classes in the FASTQ Portion of Library
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== Validation Criteria ==
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[[Category:C++]]
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=== Sequence Identifier Line ===
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[[Category:libStatGen]]
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*Every entry in the file should have a unique identifier.
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[[Category:libStatGen FASTQ]]
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=== Raw Sequence Line ===
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== Where to find the fastqFile Library and the FastQValidator ==
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*A base sequence should have non-zero length.
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*Validates the base sequences against the characters allowed via configuration.
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** Base Only: A C T G N a c t g n
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** Color Space Only: 0 1 2 3 .(period)
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** Base or Color Space: A C T G N a c t g n 0 1 2 3 .(period)
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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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=== Plus Line ===
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The fastQ Library is now a part of [[C++ Library: libStatGen]].
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=== Quality String Line ===
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The FastQValidator is documented at [[FastQValidator]].
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*A quality string should be present for every base sequence.
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*Paired quality and base sequences should be of the same length.
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*Valid quality values should all have ASCII codes > 32.
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== Additional Features ==
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== FASTQ Library Component for Reading and Validating FastQFiles ==
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*Base composition are reported and tracked by position.
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The software reads and validates fastq files in both compressed and uncompressed formats.
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*Consumes gzipped and uncompressed text files transparently (see libcsg/InputFile.h).
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== Additional Wishlist - Not Implemented ==
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The FASTQ component of the library is found in libStatGen/fastq/.
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*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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See https://github.com/statgen/libStatGen/commits/master/fastq for a list of the most recent updates to the development version of the FASTQ portion of the library.
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For the old change log, see: [[C++ Library: FASTQ Change Log]]
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== Assumptions ==
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=== Classes in the FASTQ Portion of Library ===
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{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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|-style="background: #f2f2f2; text-align: center;"
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! Class Name !!  Description
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|-
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| <code>[[C++ Class: FastQFile|FastQFile]]</code>
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| Class used for reading/validating a fastq file.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classBaseCount.html BaseCount]</code>
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| Wrapper around an array that has one index per base and an extra index for a total count of all bases.  This class is used to keep a count of the number of times each index has occurred.  It can print a percentage of the occurrence of each base against the total number of bases.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classBaseComposition.html BaseComposition]</code>
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| Class that tracks the composition of base by read location.
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|-
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| <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classFastQStatus.html FastQStatus]</code>
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| Status for FastQ operations.
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|}
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== How to Use the fastQValidator Executable ==
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== FASTQ Output ==  
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'''Required Parameters:'''
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When a sequence is read, error messages for the first maxReportedErrors are output for failed [[C++ Class: FastQFile#Validation Criteria Used For Reading a Sequence|Validation Criteria]].
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        -f :  FastQ filename with path to be prorcessed.
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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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'''Optional Parameters:'''
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== FastQValidator ==
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        -l  :  Minimum allowed read length (Defaults to 10).
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The [[FastQValidator]] was built using the FastQFile class.  More details on that program are at the supplied link.
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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:  B - ACTGN only (Default)
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                                  C - 0123. only
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                                  BC - ACTGN or 0123.
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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 BC -e 100
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        ./fastQValidator -f test/testFile.txt -l 10 -b BC -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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'''Coming Soon'''
 
Ppwhite
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