LibStatGen: FASTQ

Where to find the fastqFile Library and the FastQValidator

They are now released as part of the statgen software. Which can be downloaded at: http://genome.sph.umich.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 statgen/lib/fastq.

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 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.

Library 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.