BamUtil: dumpRefInfo - Revision history

Mktrost at 21:54, 6 January 2014

2014-01-06T21:54:43Z

← Older revision		Revision as of 17:54, 6 January 2014
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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 =
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	--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>
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	Ref ID: -1 indicates unmapped (Ref Name will be *)		Ref ID: -1 indicates unmapped (Ref Name will be *)

	~~= Usage =~~		{{paramsParameter}}
	~~./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]~~
			{{PhoneHomeParameters}}

	= Return Value =		= Return Value =

Mktrost at 14:34, 29 September 2011

2011-09-29T14:34:09Z

@@ Line 15: / Line 15: @@
          --params           : print the parameter settings
 </pre>
 = Usage =
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 *     0: the file was processed successfully.
 * non-0: the file was not processed successfully.

Mktrost: Create dumpRefInfo page

2011-09-02T18:06:05Z

Create dumpRefInfo page

New page

[[Category:BamUtil|dumpRefInfo]]
[[Category:BAM Software]]
[[Category:Software]]

= 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.

= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--printRecordRefs : print the reference information for the records in the file (grouped by reference).
--params : print the parameter settings
</pre>

= Usage =
./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]

= Return Value =
* 0: the file was processed successfully.
* non-0: the file was not processed successfully.