From Genome Analysis Wiki
Jump to navigationJump to search
1,269 bytes added
, 16:26, 6 January 2014
Line 5: |
Line 5: |
| = Overview of the <code>dumpHeader</code> function of <code>bamUtil</code> = | | = Overview of the <code>dumpHeader</code> function of <code>bamUtil</code> = |
| The <code>dumpHeader</code> option on the [[bamUtil]] executable prints the header of the specified SAM/BAM file to cout. | | The <code>dumpHeader</code> option on the [[bamUtil]] executable prints the header of the specified SAM/BAM file to cout. |
| + | |
| + | = Usage = |
| + | |
| + | ./bam dumpHeader <inputFile> |
| | | |
| = Parameters = | | = Parameters = |
Line 10: |
Line 14: |
| Required Parameters: | | Required Parameters: |
| filename : the sam/bam filename whose header should be printed. | | filename : the sam/bam filename whose header should be printed. |
| + | </pre> |
| + | <pre> |
| + | PhoneHome: |
| + | --noPhoneHome : disable PhoneHome (default enabled) |
| </pre> | | </pre> |
| | | |
− | = Usage = | + | == 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. |
| + | |
| + | A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM). |
| + | |
| + | {|border="1" cellspacing="0" cellpadding="2" |
| + | |SAM/BAM/Uncompressed BAM from file |
| + | | <code>yourFileName</code> |
| + | |- |
| + | |SAM from stdin |
| + | | <code>-</code> |
| + | |- |
| + | |BAM from stdin |
| + | | <code>-.bam</code> |
| + | |- |
| + | |Uncompressed BAM from stdin |
| + | | <code>-.ubam</code> |
| + | |} |
| + | |
| + | Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported. |
| + | |
| + | == Phone Home Parameters == |
| + | See [[PhoneHome]] for more information on how PhoneHome works and what it does. |
| | | |
− | ./bam dumpHeader <inputFile>
| + | === Turn off PhoneHome (<code>--noPhoneHome</code>) === |
| + | Use the <code>--noPhoneHome</code> option to completely disable PhoneHome. PhoneHome is enabled by default based on the default thinning parameter. |
| | | |
| = Return Value = | | = Return Value = |