Difference between revisions of "LibStatGen: FASTQ"
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| + | [[Category:C++]] | ||
| + | [[Category:libStatGen]] | ||
| + | [[Category:libStatGen FASTQ]] | ||
| + | |||
== Where to find the fastqFile Library and the FastQValidator == | == Where to find the fastqFile Library and the FastQValidator == | ||
| − | + | ||
| + | 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 | + | The FASTQ component of the library is found in libStatGen/fastq/. |
| − | See | + | 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. |
| − | === Classes in the FASTQ Library === | + | For the old change log, see: [[C++ Library: FASTQ Change Log]] |
| + | |||
| + | === Classes in the FASTQ Portion of Library === | ||
{| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | {| style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | ||
|-style="background: #f2f2f2; text-align: center;" | |-style="background: #f2f2f2; text-align: center;" | ||
| Line 17: | Line 26: | ||
| Class used for reading/validating a fastq file. | | Class used for reading/validating a fastq file. | ||
|- | |- | ||
| − | | <code>BaseCount</code> | + | | <code>[http://csg.sph.umich.edu//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://csg.sph.umich.edu//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. | ||
| + | |- | ||
| + | | <code>[http://csg.sph.umich.edu//mktrost/doxygen/current/classFastQStatus.html FastQStatus]</code> | ||
| + | | Status for FastQ operations. | ||
|} | |} | ||
| − | + | == 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]]. |
| − | When a sequence is read, error messages for the first maxReportedErrors are output for failed [[#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. | ||
ERROR on Line 29: First line of a sequence does not begin wtih @ | ERROR on Line 29: First line of a sequence does not begin wtih @ | ||
ERROR on Line 33: No Sequence Identifier specified before the comment. | ERROR on Line 33: No Sequence Identifier specified before the comment. | ||
| − | |||
== FastQValidator == | == FastQValidator == | ||
The [[FastQValidator]] was built using the FastQFile class. More details on that program are at the supplied link. | The [[FastQValidator]] was built using the FastQFile class. More details on that program are at the supplied link. | ||
Latest revision as of 10:49, 2 February 2017
Where to find the fastqFile Library and the FastQValidator
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
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/libStatGen/commits/master/fastq 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
| 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. |
FastQStatus
|
Status for FastQ operations. |
FASTQ 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.
