Difference between revisions of "BamUtil: readReference"

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= Overview of the <code>readReference</code> function of <code>bamUtil</code> =
 
= Overview of the <code>readReference</code> function of <code>bamUtil</code> =
 
The <code>readReference</code> option on the [[bamUtil]] executable prints the specified region of the reference sequence in an easy to read format.
 
The <code>readReference</code> option on the [[bamUtil]] executable prints the specified region of the reference sequence in an easy to read format.
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= Usage =
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./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
  
 
= Parameters =
 
= Parameters =
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--numBases : number of bases from start to display
 
--numBases : number of bases from start to display
 
</pre>
 
</pre>
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{{PhoneHomeParamDesc}}
  
= Usage =
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== Required Parameters ==
./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
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{{RefFile}}
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=== Reference Name (<code>--refName</code>) ===
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The Reference/Chromosome Name to read from the reference file.
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=== Start Position (<code>--start</code>) ===
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Use <code>--start</code> to specify the 0-based position to start printing bases from.
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=== Length Parameters (<code>--end</code>, <code>--numBases</code>) ===
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The length of the reference to be printed must be specified.
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Use <code>--end</code> to indicate the exclusive 0-based end position.
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:OR (but not both)
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Use <code>--numBases</code> to indicate the number of bases to display.
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{{paramsParameter}}
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{{PhoneHomeParameters}}
  
 
= Return Value =
 
= Return Value =

Latest revision as of 18:07, 6 January 2014


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.

Example Output