BamUtil: dumpIndex

Overview of the dumpIndex function of bamUtil

The dumpIndex option on the bamUtil executable prints BAM index file in an easy to read format.

Usage

./bam dumpIndex --bamIndex <bamIndexFile> [--refID <ref#>] [--summary] [--params]

Parameters

    Required Parameters:
        --bamIndex : the path/name of the bam index file to display
    Optional Parameters:
        --refID    : the reference ID to read, defaults to print all
        --summary  : only print a summary - 1 line per reference.
        --params   : print the parameter settings

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

Required Parameters

Bam Index File (--bamIndex)

Use --bamIndex followed by your file name to specify the BAM index file to use for reading the BAM file.

Optional Parameters

Only dump a single Reference ID (--refID)

Use --refID followed by a reference ID to only print the information for that reference ID.

By default, information for all reference IDs are printed.

Print Summaries Only (--summary)

Use --summary to print only a 1 line summary for each reference ID rather than the full output.

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 BAM index file was processed successfully.
• non-0: the BAM index file was not processed successfully.