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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 == |
− | 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]]. |
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| == 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. |
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− | The FASTQ component of the library is found in statgen/lib/fastq. | + | The FASTQ component of the library is found in libStatGen/fastq/. |
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− | 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. | + | 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. |
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− | === 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;" |
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| | 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. |
| |} | | |} |
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− | | + | == FASTQ Output == |
− | == Library 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. |
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| == 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. |