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LibStatGen: FASTQ (view source)

Revision as of 17:33, 6 April 2010

404 bytes added ,  17:33, 6 April 2010
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The fastQFile and FastQValidator code can be downloaded at: http://www.sph.umich.edu/csg/mktrost/fastQFile/
 
The fastQFile and FastQValidator code can be downloaded at: http://www.sph.umich.edu/csg/mktrost/fastQFile/
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== How to Use the fastQFile Library ==
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== FastQFile Library for Reading and Validating FastQFiles ==
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*'''Library Name:''' libfqf.a
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The software reads and validates fastq files in both compressed and uncompressed formats.
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*'''Additional Libraries Needed:''' libcsg/libcsg.a thirdParty/samtools/libbam.a
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**Note: When you include the libraries, make sure you include them in this order:
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The library is found in pipeline/bam, and is called libfqf.a.
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This library is dependent on two other libraries, [[C++ Library: libcsg|libcsg/libcsg.a]] and samtools/libbam.a so be sure to include them all in the proper order:
 
  <path to base pipeline directory>/fastQFile/libfqf.a <path to base pipeline directory>/libcsg/libcsg.a <path to base pipeline directory>/thirdParty/samtools/libbam.a
 
  <path to base pipeline directory>/fastQFile/libfqf.a <path to base pipeline directory>/libcsg/libcsg.a <path to base pipeline directory>/thirdParty/samtools/libbam.a
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*'''Include Files:''' FastQFile.h
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*'''Class Name:''' FastQFile
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=== Classes in the FastQFile 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>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>BaseComposition</code>
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| Class that tracks the composition of base by read location.
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|}
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** Constructor Parameters:
 
** Constructor Parameters:
 
*** int minReadLength - The minimum length that a base sequence must be for it to be valid.
 
*** int minReadLength - The minimum length that a base sequence must be for it to be valid.
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== Libraries & Classes ==
 
== Libraries & Classes ==
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*libfqf.a
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**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.
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**BaseComposition - class that tracks the composition of base by read location.
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**FastQFile - class that reads/validates a fastq file.
   
*libcsg.a
 
*libcsg.a
 
**String (StringBasics) - String class for string operations
 
**String (StringBasics) - String class for string operations
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/954"

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