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== Reading/Writing SAM/BAM Files In Your Program ==
== Reading/Writing SAM/BAM Files In Your Program ==
The '''SamFile''' class allows a user to easily read/write a SAM/BAM file.
=== Reading/Writing Standard SAM/BAM Files ===
=== Reading/Writing Standard SAM/BAM Files ===
The methods found in this class are:
The methods found in this class are:
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==== Usage Example ====
==== Usage Example ====
The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file. The file format of the output sam/bam file is determined by the '''SamFile''' class based on the extension of the output file. A ".bam" extension indicates a BAM file. All other extensions indicate SAM files.
The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined by the SamFile class based on reading the type from the file. The file format of the output sam/bam file is determined by the '''SamFile''' class based on the extension of the output file. A ".bam" extension indicates a BAM file. All other extensions indicate SAM files.
<pre>
<source lang="cpp">
int main(int argc, char ** argv)
int main(int argc, char ** argv)
{
{
std::cout << "Number of valid records = " << numValidRecords << std::endl;
std::cout << "Number of valid records = " << numValidRecords << std::endl;
}
}
</pre>
</source>
==== Usage Example ====
==== Usage Example ====
This example reads in the inputFilename bam file and writes it back out section by section to the specified outputFilename, starting with section -1. It also prints a count of the number of records in each section.
This example reads in the inputFilename bam file and writes it back out section by section to the specified outputFilename, starting with section -1. It also prints a count of the number of records in each section.
<pre>
<source lang="cpp">
int ReadIndexedBam(const char* inputFilename,
int ReadIndexedBam(const char* inputFilename,
const char* outputFilename,
const char* outputFilename,
return(0);
return(0);
}
}
</pre>
</source>
