Mktrost at 21:48, 6 January 2014

2014-01-06T21:48:20Z

← Older revision		Revision as of 21:48, 6 January 2014
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	For more flexibility of writing specific regions, see [[BamUtil: writeRegion]].		For more flexibility of writing specific regions, see [[BamUtil: writeRegion]].

			= Usage =
			./bam readIndexedBam <inputFilename> <outputFile.sam/bam> <bamIndexFile>

	= Parameters =		= Parameters =
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	outputFile.sam/bam - path/name of the output file		outputFile.sam/bam - path/name of the output file
	bamIndexFile - path/name of the BAM index file		bamIndexFile - path/name of the BAM index file
			</pre>
			<pre>
			PhoneHome:
			--noPhoneHome : disable PhoneHome (default enabled)
	</pre>		</pre>

	= ~~Usage~~ =		== Required Parameters ==
	.~~/bam readIndexedBam~~ <~~inputFilename~~> <~~outputFile.sam~~/~~bam~~> <~~bamIndexFile~~>		{{InBAMInputFile\|noParam=1st}}
			{{OutBAMOutputFile\|noParam=2nd}}
			{{BamIndex\|noParam=3rd\|required=1}}

			== Phone Home Parameters ==
			See [[PhoneHome]] for more information on how PhoneHome works and what it does.

			=== Turn off PhoneHome (<code>--noPhoneHome</code>) ===
			Use the <code>--noPhoneHome</code> option to completely disable PhoneHome. PhoneHome is enabled by default based on the default thinning parameter.

	= Return Value =		= Return Value =
	* 0		* 0

Mktrost: Create page for readIndexedBam

2011-09-02T18:10:45Z

Create page for readIndexedBam

New page

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

= Overview of the <code>readIndexedBam</code> function of <code>bamUtil</code> =
The <code>readIndexedBam</code> option on the [[bamUtil]] executable reads an indexed BAM file reference id by reference id, from -1 to the max reference id and writes it out as a SAM/BAM file.

For more flexibility of writing specific regions, see [[BamUtil: writeRegion]].

= Parameters =
<pre>
Required Parameters:
inputFilename - path/name of the input BAM file
outputFile.sam/bam - path/name of the output file
bamIndexFile - path/name of the BAM index file
</pre>

= Usage =
./bam readIndexedBam <inputFilename> <outputFile.sam/bam> <bamIndexFile>

= Return Value =
* 0

BamUtil: readIndexedBam - Revision history

Mktrost at 21:48, 6 January 2014

Mktrost: Create page for readIndexedBam