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= 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 =
Required Parameters:
Required Parameters:
filename : the sam/bam filename whose header should be printed.
filename : the sam/bam filename whose header should be printed.
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PhoneHome:
--noPhoneHome : disable PhoneHome (default enabled)
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= 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.
=== 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 =
