BamUtil
bam Executable
When the pipeline is compiled, the SAM/BAM executable, "bam" is generated in the pipeline/bam/ directory.
The software reads the beginning of an input file to determine if it is SAM/BAM. To determine the format (SAM/BAM) of the output file, the software checks the output file's extension. If the extension is ".bam" it writes a BAM file, otherwise it writes a SAM file.
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
This executable is built using the bam library.
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.
Example Output
Read a SAM/BAM file and write as a SAM/BAM file
This executable takes 2 arguments. The first argument is the input file. The second argument is the output file. The executable converts the first file into the format of the second file. So if you want to convert a BAM file to a SAM file, from the pipeline/bam/ directory you just call:
./bam <bamFile>.bam <newSamFile>.sam
Don't forget to put in the paths to the executable and your test files.
Usage
./bam <inputFile> <outputFile.sam/bam>
Return Value
Example Output
Dump a BAM index file
Usage
./bam dump_index <bamIndexFile>
Return Value
- -1 if the bam index file could not be opened.
- 0 if the bam index file could be opened.
Example Output
Read & Write indexed BAM file
Usage
./bam read_indexed_bam <inputFilename> <outputFile.sam/bam> <bamIndexFile>
Return Value
- 0
