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= Overview of the <code>readReference</code> function of <code>bamUtil</code> =
= 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.
The <code>readReference</code> option on the [[bamUtil]] executable prints the specified region of the reference sequence in an easy to read format.
= Usage =
./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
= Parameters =
= Parameters =
--numBases : number of bases from start to display
--numBases : number of bases from start to display
</pre>
</pre>
{{PhoneHomeParamDesc}}
= Usage =
== Required Parameters ==
{{RefFile}}
=== Reference Name (<code>--refName</code>) ===
The Reference/Chromosome Name to read from the reference file.
=== Start Position (<code>--start</code>) ===
Use <code>--start</code> to specify the 0-based position to start printing bases from.
=== Length Parameters (<code>--end</code>, <code>--numBases</code>) ===
The length of the reference to be printed must be specified.
Use <code>--end</code> to indicate the exclusive 0-based end position.
:OR (but not both)
Use <code>--numBases</code> to indicate the number of bases to display.
{{paramsParameter}}
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
