BamUtil: readReference

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Overview of the readReference function of bamUtil

The readReference option on the bamUtil executable prints the specified region of the reference sequence in an easy to read format.

Parameters

	Required Parameters:
		--refFile  : the reference
		--refName  : the SAM/BAM reference Name to read
		--start    : inclusive 0-based start position
		--params   : print the parameter settings
	Required Length Parameter (one but not both needs to be specified):
		--end      : exclusive 0-based end position
		--numBases : number of bases from start to display

Usage

./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]

Return Value

  • 0: the reference file was successfully read.
  • non-0: the reference file was not successfully read.

Example Output