Changes

From Genome Analysis Wiki
Jump to navigationJump to search

LibStatGen: FASTQ (view source)

Revision as of 16:33, 6 April 2010

404 bytes added ,  16:33, 6 April 2010
no edit summary
Line 2: Line 2:  
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/
   −
== How to Use the fastQFile Library ==
+
== FastQFile Library for Reading and Validating FastQFiles ==
−
*'''Library Name:''' libfqf.a
+
The software reads and validates fastq files in both compressed and uncompressed formats.
−
*'''Additional Libraries Needed:''' libcsg/libcsg.a thirdParty/samtools/libbam.a
+
 
−
**Note: When you include the libraries, make sure you include them in this order:
+
The library is found in pipeline/bam, and is called libfqf.a.
 +
 
 +
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
−
*'''Include Files:''' FastQFile.h
+
 
−
*'''Class Name:''' FastQFile
+
=== 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: center;"
 +
! 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:
 
** 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.
Line 77: Line 93:     
== Libraries & Classes ==
 
== 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
 
*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"

Navigation menu