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Revision as of 14:23, 2 September 2011
, 14:23, 2 September 2011Add readReference
[[Category:BamUtil|readReference]]
[[Category:BAM Software]]
[[Category:Software]]
= Overview of the <code>readReference</code> function of <code>bamUtil</code> =
The <code>readReference</code> option on the [[bamUtil]] executable prints the specified region of the reference sequence in an easy to read format.
= Parameters =
<pre>
Required Parameters:
--refFile : the reference
--refName : the SAM/BAM reference Name to read
--start : inclusive 0-based start position
--params : print the parameter settings
Required Length Parameter (one but not both needs to be specified):
--end : exclusive 0-based end position
--numBases : number of bases from start to display
</pre>
= Usage =
./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
= Return Value =
* 0: the reference file was successfully read.
* non-0: the reference file was not successfully read.
= Example Output =
<pre>
</pre>
[[Category:BAM Software]]
[[Category:Software]]
= Overview of the <code>readReference</code> function of <code>bamUtil</code> =
The <code>readReference</code> option on the [[bamUtil]] executable prints the specified region of the reference sequence in an easy to read format.
= Parameters =
<pre>
Required Parameters:
--refFile : the reference
--refName : the SAM/BAM reference Name to read
--start : inclusive 0-based start position
--params : print the parameter settings
Required Length Parameter (one but not both needs to be specified):
--end : exclusive 0-based end position
--numBases : number of bases from start to display
</pre>
= Usage =
./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
= Return Value =
* 0: the reference file was successfully read.
* non-0: the reference file was not successfully read.
= Example Output =
<pre>
</pre>
