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
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.
./bam validate --in <inputFile> [--so_flag|--so_unsorted|--so_coord|--so_query]
- 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.