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= Overview of the <code>dumpRefInfo</code> function of <code>bamUtil</code> =
= 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.
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 =
= Parameters =
--params : print the parameter settings
--params : print the parameter settings
</pre>
</pre>
{{PhoneHomeParamDesc}}
== Required Parameters ==
{{InBAMInputFile}}
printRecordRefs outputs the id, the name, and the number of records with that id/name in the SAM/BAM file.
== Optional Parameters ==
{{noeofBGZFParameter}}
=== Print Number of Records for each Chromosome (<code>--printRecordRefs</code>) ===
Use the <code>--printRecordRefs</code> option to also output each reference/chromsome id, name, and the number of records with that id/name in the SAM/BAM file.
Example:
Example:
<pre>
<pre>
Ref ID: -1 indicates unmapped (Ref Name will be *)
Ref ID: -1 indicates unmapped (Ref Name will be *)
{{paramsParameter}}
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
