Changes

== Where to find the fastqFile Library and the FastQValidator ==

== 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

 

The fastQ Library is now a part of [[C++ Library: libStatGen]].

 

The FastQValidator is documented at [[FastQValidator]].

== FASTQ Library Component for Reading and Validating FastQFiles ==

== FASTQ Library Component for Reading and Validating FastQFiles ==

The software reads and validates fastq files in both compressed and uncompressed formats.

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.

The FASTQ component of the library is found in libStatGen/fastq/.

 

See https://github.com/statgen/libStatGen/commits/master/fastq for a list of the most recent updates to the development version of the FASTQ portion of the library.

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.

For the old change log, see: [[C++ Library: FASTQ Change Log]]

=== Classes in the FASTQ Portion of Library ===

=== Classes in the FASTQ Portion of Library ===

| Class used for reading/validating a fastq file.

| Class used for reading/validating a fastq file.

|-

|-

| <code>BaseCount</code>

| <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.

| 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>

| <code>[http://www.sph.umich.edu/csg/mktrost/doxygen/current/classBaseComposition.html BaseComposition]</code>

| Class that tracks the composition of base by read location.

| Class that tracks the composition of base by read location.

|}

|}

== FASTQ Output ==  

== FASTQ Output ==  

When a sequence is read, error messages for the first maxReportedErrors are output for failed [[#Validation Criteria Used For Reading a Sequence|Validation Criteria]].

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:

For Example:

  ERROR on Line 25: The sequence identifier line was too short.

  ERROR on Line 25: The sequence identifier line was too short.