Difference between revisions of "LibStatGen: FASTQ"

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(Created page with '== How to Use the fastQValidator Executable == '''Required Parameters:''' -f : FastQ filename with path to be prorcessed. '''Optional Parameters:''' -l : Min…')
 
(Classes in the FASTQ Portion of Library)
 
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== How to Use the fastQValidator Executable ==
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[[Category:C++]]
'''Required Parameters:'''
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[[Category:libStatGen]]
        -f  : FastQ filename with path to be prorcessed.
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[[Category:libStatGen FASTQ]]
  
'''Optional Parameters:'''
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== Where to find the fastqFile Library and the FastQValidator ==
        -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:  B - ACTGN only (Default)
 
                                  C - 0123. only
 
                                  BC - ACTGN or 0123.
 
  
'''Testing only Parameters:'''
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The fastQ Library is now a part of [[C++ Library: libStatGen]].
        -t  :  If "ReadOnly" is specified, the fastq will be read but not processed.  This may be used for determining read time.
 
'''Usage:'''
 
        ./fastQValidator -f <fileName> -l <minReadLen> -e <maxReprotedErrors> -b <rawSeqType>
 
  
'''Examples:'''
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The FastQValidator is documented at [[FastQValidator]].
        ../fastQValidator -f testFile.txt
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        ../fastQValidator -f testFile.txt -l 10 -b BC -e 100
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== FASTQ Library Component for Reading and Validating FastQFiles ==
        ./fastQValidator -f test/testFile.txt -l 10 -b BC -e 100
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The software reads and validates fastq files in both compressed and uncompressed formats.
        time ./fastQValidator -f test/testFile.txt -t ReadOnly
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The FASTQ component of the library is found in libStatGen/fastq/.
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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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=== 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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== FASTQ Output ==
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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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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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== FastQValidator ==
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The [[FastQValidator]] was built using the FastQFile class.  More details on that program are at the supplied link.

Latest revision as of 10:49, 2 February 2017


Where to find the fastqFile Library and the FastQValidator

The fastQ Library is now a part of C++ Library: libStatGen.

The FastQValidator is documented at FastQValidator.

FASTQ Library Component for Reading and Validating FastQFiles

The software reads and validates fastq files in both compressed and uncompressed formats.

The FASTQ component of the library is found in libStatGen/fastq/.

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.

For the old change log, see: C++ Library: FASTQ Change Log

Classes in the FASTQ Portion of Library

Class Name Description
FastQFile Class used for reading/validating a fastq file.
BaseCount 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.
BaseComposition Class that tracks the composition of base by read location.
FastQStatus Status for FastQ operations.

FASTQ Output

When a sequence is read, error messages for the first maxReportedErrors are output for failed Validation Criteria. For Example:

ERROR on Line 25: The sequence identifier line was too short.
ERROR on Line 29: First line of a sequence does not begin wtih @
ERROR on Line 33: No Sequence Identifier specified before the comment.

FastQValidator

The FastQValidator was built using the FastQFile class. More details on that program are at the supplied link.