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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 =
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
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PhoneHome:
--noPhoneHome : disable PhoneHome (default enabled)
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= 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
