Difference between revisions of "BamUtil"
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The bam executable has the following functions. | The bam executable has the following functions. | ||
* [[C++ Executable: bam#Read and Validate a SAM/BAM file|Read and Validate a SAM/BAM file]] | * [[C++ Executable: bam#Read and Validate a SAM/BAM file|Read and Validate a SAM/BAM file]] | ||
| − | * Read a SAM/BAM file and write | + | * [[C++ Executable: bam#Read a SAM/BAM file and write as 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. | + | * [[C++ Executable: bam#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. | + | * [[C++ Executable: bam#Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file. |
Revision as of 11:58, 6 April 2010
bam Executable
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
- [[C++ Executable: bam#Dump a BAM index file into an easy to read text version.
- [[C++ Executable: bam#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.
