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LibStatGen: FASTQ

252 bytes added, 12:41, 7 September 2011
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== Where to find the fastqFile Library and the FastQValidator ==
They are The fastQ Library is now released as a part of the statgen software[[C++ Library: libStatGen]]. Which can be downloaded  The FastQValidator is documented at: http://genome.sph.umich[[FastQValidator]].edu/wiki/Software#Download
== 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/liblibStatGen/commits/master/fastqfor a list of the most recent updates to the development version of the FASTQ portion of the library.
See For the old change log, see: [[C++ Library: FASTQ Change Log]] for a list of the most recent updates to the development version of the FASTQ portion of the library.
=== Classes in the FASTQ Portion of Library ===
| Class used for reading/validating a fastq file.
|-
| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classBaseCount.html 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>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classBaseComposition.html BaseComposition]</code>
| Class that tracks the composition of base by read location.
|}
== FASTQ Output ==
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]].
For Example:
ERROR on Line 25: The sequence identifier line was too short.

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