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BamUtil: dumpRefInfo

304 bytes added, 16:54, 6 January 2014
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= Overview of the <code>dumpRefInfo</code> function of <code>bamUtil</code> =
The <code>dumpRefInfo</code> option on the [[bamUtil]] executable prints the SAM/BAM file's reference information.
 
= Usage =
./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]
= Parameters =
--params : print the parameter settings
</pre>
{{PhoneHomeParamDesc}}
== Required Parameters ==
{{InBAMInputFile}}
== Optional Parameters =={{noeofBGZFParameter}} === Print Number of Records for each Chromosome (<code>--printRecordRefs outputs </code>) ===Use the <code>--printRecordRefs</code> option to also output each reference/chromsome id, the name, and the number of records with that id/name in the SAM/BAM file.
Example:
<pre>
Ref ID: -1 indicates unmapped (Ref Name will be *)
= Usage ={{paramsParameter}} ./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]{{PhoneHomeParameters}}
= Return Value =

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