Mktrost at 22:07, 6 January 2014

2014-01-06T22:07:29Z

@@ Line 5: / Line 5: @@
 = 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 =
@@ Line 17: / Line 20: @@
 		--numBases : number of bases from start to display
 </pre>
-= Usage =
+== Required Parameters ==
- ./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
+{{RefFile}}
 = Return Value =

Mktrost: Add readReference

2011-09-02T18:23:12Z

Add readReference

New page

[[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>

BamUtil: readReference - Revision history

Mktrost at 22:07, 6 January 2014

Mktrost: Add readReference