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LibStatGen: FASTQ

404 bytes added, 16:33, 6 April 2010
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The fastQFile and FastQValidator code can be downloaded at: http://www.sph.umich.edu/csg/mktrost/fastQFile/
== How to Use the fastQFile FastQFile Library for Reading and Validating FastQFiles ==*'''Library Name:''' The software reads and validates fastq files in both compressed and uncompressed formats. The library is found in pipeline/bam, and is called libfqf.a. *'''Additional Libraries NeededThis library is dependent on two other libraries, [[C++ Library:''' libcsg|libcsg/libcsg.a thirdParty/]] and samtools/libbam.a**Note: When you include the libraries, make so be sure you to include them all in this 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
*'''Include Files=== Classes in the FastQFile Library ==={| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"|-style="background: #f2f2f2; text-align:''' FastQFile.hcenter;"*'''! Class Name!! Description|-| <code>[[C++ Class:''' FastQFile|FastQFile]]</code>| Class used for reading/validating a fastq file.|-| <code>BaseCount</code>| 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.|-| <code>BaseComposition</code>| Class that tracks the composition of base by read location.|} 
** Constructor Parameters:
*** int minReadLength - The minimum length that a base sequence must be for it to be valid.
== Libraries & Classes ==
*libfqf.a
**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.
**FastQFile - class that reads/validates a fastq file.
*libcsg.a
**String (StringBasics) - String class for string operations

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