Difference between revisions of "BamUtil"
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* [[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]] | ||
* [[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]] | * [[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]] | ||
| − | * [[C++ Executable: bam#Dump a BAM index file into an easy to read text version | + | * [[C++ Executable: bam#Dump a BAM index file|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 | + | * [[C++ Executable: bam#Read & Write indexed BAM file|Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file]] |
| Line 25: | Line 25: | ||
* non-0: at least one record was not successfully read, not valid, or not 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 == | ||
| + | |||
| + | === 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 | ||
=== Example Output === | === Example Output === | ||
Revision as of 13:43, 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
- 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.
Example Output
Read a SAM/BAM file and write as a SAM/BAM file
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
