= bam Executable = The bam executable has the following functions. * [[C++ Executable: bam#Read and Validate a SAM/BAM file|Read and Validate a SAM/BAM file]] * Read a SAM/BAM file and write the same SAM/BAM file. * Dump a BAM index file into an easy to read text version. * Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file.
== Read and Validate a SAM/BAM file ==
The <code>validate</code> option on the bam executable validates a SAM/BAM file.
The validation checks that the file is sorted as specified in the user options. Default is unsorted, in which case, no order validation is done.
'''NOTE: Currently the only validation that is done is that the file is sorted as specified in the user specified options. '''
= Usage ===
./bam validate --in <inputFile> [--so_flag|--so_unsorted|--so_coord|--so_query]
=== Return Value === * 0: all records are successfully read, are valid, and are properly sorted. * non-0: at least one record was not successfully read, not valid, or not properly sorted.
Example Output = ==