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 the same 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]]
* 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

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