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BamUtil: readReference

653 bytes added, 18:07, 6 January 2014
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= 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.
 
= Usage =
./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
= Parameters =
--numBases : number of bases from start to display
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{{PhoneHomeParamDesc}}
= Usage =Required Parameters =={{RefFile}}  ./bam readReference === Reference Name (<code>--refFile refName</code>) ===The Reference/Chromosome Name to read from the reference file. === Start Position (<referenceFilenamecode> --refName start</code>) ===Use <reference Namecode> --start </code> to specify the 0 -based position to startprinting 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 endposition. :OR (but not both) Use <code>|--numBases </code> to indicate the number of bases> [--params]to display. {{paramsParameter}} {{PhoneHomeParameters}}
= Return Value =

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