The bam executable has the following functions.
- Read and Validate a SAM/BAM file
- Read a SAM/BAM file and write as a 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.
Read a SAM/BAM file and write as a SAM/BAM file
./bam <inputFile> <outputFile.sam/bam>
Dump a BAM index file
./bam dump_index <bamIndexFile>
- -1 if the bam index file could not be opened.
- 0 if the bam index file could be opened.
Read & Write indexed BAM file
./bam read_indexed_bam <inputFilename> <outputFile.sam/bam> <bamIndexFile>