BamUtil: explainFlags

From Genome Analysis Wiki
Jump to: navigation, search


Overview of the explainFlags function of bamUtil

The explainFlags option on the bamUtil executable prints a text description of the specified flag value.

This function was added in version 1.0.10.

Usage

./bam explainFlags --hex|dec <flag> [--params]

Parameters

	FlagValue Parameters:
		--hex     : Explain this hex flag
		--dec     : Explain this decimal flag
		--params  : print the parameter settings
	PhoneHome:
		--noPhoneHome       : disable PhoneHome (default enabled)
		--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)

Required Parameters

Flag Value (--hex, --dec)

The flag to translate to text can be either a decimal integer or a hex number.

Use --dec to translate a decimal integer.

Use --hex to translate a hex number. The hex number can be specified with or without the preceding "0x", producing the same result either way.

Optional Parameters

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 on success, non-0 on error.

Example Output

bin/bam explainFlags --hex 0x70C

0x70c (1804):
	unmapped
	mate unmapped
	unknown fragment
	secondary alignment
	fails QC checks
	duplicate

Number of records read = 10
Number of records written = 10

bin/bam explainFlags --hex 704

0x704 (1796):
	unmapped
	unknown fragment
	secondary alignment
	fails QC checks
	duplicate

bin/bam explainFlags --dec 1804

0x70c (1804):
	unmapped
	mate unmapped
	unknown fragment
	secondary alignment
	fails QC checks
	duplicate