Overview of the
dumpHeader function of
dumpHeader option on the bamUtil executable prints the header of the specified SAM/BAM file to cout.
./bam dumpHeader <inputFile>
Required Parameters: filename : the sam/bam filename whose header should be printed.
PhoneHome: --noPhoneHome : disable PhoneHome (default enabled)
Input File (1st Parameter)
The 1st argumentis the input SAM/BAM file. The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.
- is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).
|SAM/BAM/Uncompressed BAM from file|| |
|SAM from stdin|| |
|BAM from stdin|| |
|Uncompressed BAM from stdin|| |
Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the
samtools implementation so pipes between our tools and
samtools are supported.
Phone Home Parameters
See PhoneHome for more information on how PhoneHome works and what it does.
Turn off PhoneHome (
--noPhoneHome option to completely disable PhoneHome. PhoneHome is enabled by default based on the default thinning parameter.
- 0: the header was successfully read and printed.
- non-0: the header was not successfully read or was not printed. (Returns the SamStatus.)
@SQ SN:1 LN:247249719 @SQ SN:2 LN:242951149 @SQ SN:3 LN:199501827