BamUtil

bam Executable

The bam executable has the following functions.

• 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 validate 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.