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== How to Use the fastQFile Library ==
== How to Use the fastQFile Library ==
*'''Library Name:''' libfqf.a
*'''Library Name:''' libfqf.a
*'''Additional Libraries Needed:''' libcsg.a
*'''Additional Libraries Needed:''' libcsg/libcsg.a thirdParty/samtools/libbam.a
**Note: When you include the libraries, make sure you include them in this order:
<path to base pipeline directory>/fastQFile/libfqf.a <path to base pipeline directory>/libcsg/libcsg.a <path to base pipeline directory>/thirdParty/samtools/libbam.a
*'''Include Files:''' FastQFile.h
*'''Include Files:''' FastQFile.h
*'''Class Name:''' FastQFile
*'''Class Name:''' FastQFile
Here is an example of how this would be done.
Here is an example of how this would be done.
FastQFile fastQFile;
String filename = <your filename>;
String filename = <your filename>;
// Open the fastqfile with the default UNKNOWN space type which will determine the
// Open the fastqfile.
// base type from the first character in the sequence.
if(openFile(filename, spaceType) != FASTQ_SUCCESS)
if(fastQFile.openFile(filename) != FASTQ_SUCCESS)
{
{
// Failed to open the specified file.
// Failed to open the specified file.
}
}
// Keep reading the file until there are no more fastq sequences to process.
// Keep reading the file until there are no more fastq sequences to process.
while (!ifeof(myFile))
while (!fastQFile.isEof())
{
{
// Read one sequence. This call will read all the lines for
// Read one sequence. This call will read all the lines for
// one sequence.
// one sequence.
/////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////
// NOTE: It is up to you if you want to process only for success:
// NOTE: It is up to you if you want to process only for success:
// Do NOT try to process on a FASTQ_FAILURE
// Do NOT try to process on a FASTQ_FAILURE
/////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////
if(readFastQSequence() == FASTQ_SUCCESS)
if(fastQFile.readFastQSequence() == FastQFile::FASTQ_SUCCESS)
{
{
// The sequence is valid.
// The sequence is valid.
<Your Processing Here>
<Your Processing Here>
// For example if you want to print the lines of the sequence:
printf("The Sequence ID Line is: %s", fastQFile.mySequenceIdLine.c_str());
printf("The Sequence ID is: %s", fastQFile.mySequenceIdentifier.c_str());
printf("The Sequence Line is: %s", fastQFile.myRawSequence.c_str());
printf("The Plus Line is: %s", fastQFile.myPlusLine.c_str());
printf("The Quality String Line is: %s", fastQFile.myQualityString.c_str());
}
}
}
}
// Finished processing all of the sequences in the file.
// Finished processing all of the sequences in the file.
// Close the input file.
// Close the input file.
closeFile();
fastQFile.closeFile();
return(<your return info>); // It is up to you to determine your return.
return(<your return info>); // It is up to you to determine your return.
== Validation Criteria Used For Reading a Sequence ==
== Validation Criteria Used For Reading a Sequence ==
