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== Simple Read/Write SAM/BAM 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.
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.
== Simple Read/Write Indexed BAM Files ==
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.
<source lang="cpp">
<source lang="cpp">
</source>
</source>
== Validate SAM/BAM Files Continuing Processing After Allowed Errors ==
This example demonstrates calling validation on a SAM/BAM file. It also demonstrates a more complicated read loop that continues until a configurable number of errors are hit.
This example demonstrates calling validation on a SAM/BAM file. It also demonstrates a more complicated read loop that continues until a configurable number of errors are hit.
<source lang="cpp">
<source lang="cpp">
