BamUtil: readReference

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.

Usage

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

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

	PhoneHome:
		--noPhoneHome       : disable PhoneHome (default enabled)
		--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)

Required Parameters

Reference File (--refFile)

Use --refFile followed by the reference file name to specify the reference sequence file.

Reference Name (--refName)

The Reference/Chromosome Name to read from the reference file.

Start Position (--start)

Use --start to specify the 0-based position to start printing bases from.

Length Parameters (--end, --numBases)

The length of the reference to be printed must be specified.

Use --end to indicate the exclusive 0-based end position.

OR (but not both)

Use --numBases to indicate the number of bases to display.

Print the Program Parameters (--params)

Use --params to print the parameters for your program to stderr.

PhoneHome Parameters

See PhoneHome for more information on how PhoneHome works and what it does.

Turn off PhoneHome (--noPhoneHome)

Use the --noPhoneHome option to completely disable PhoneHome. PhoneHome is enabled by default based on the thinning parameter.

Adjust the Frequency of PhoneHome (--phoneHomeThinning)

Use --phoneHomeThinning to modify the percentage of the time that PhoneHome will run (0-100).

• By default, --phoneHomeThinning is set to 50, running 50% of the time.
• PhoneHome will only occur if the run's random number modulo 100 is less than the --phoneHomeThinning value.
• N/A if --noPhoneHome is set.

Return Value

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