Difference between revisions of "BamUtil: dumpIndex"
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= Overview of the <code>dumpIndex</code> function of <code>bamUtil</code> = | = Overview of the <code>dumpIndex</code> function of <code>bamUtil</code> = | ||
The <code>dumpIndex</code> option on the [[bamUtil]] executable prints BAM index file in an easy to read format. | The <code>dumpIndex</code> 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 = | = Parameters = | ||
| Line 15: | Line 18: | ||
--params : print the parameter settings | --params : print the parameter settings | ||
</pre> | </pre> | ||
| + | {{PhoneHomeParamDesc}} | ||
| + | |||
| + | == Required Parameters == | ||
| + | {{BamIndex|required=1}} | ||
| + | |||
| + | == Optional Parameters == | ||
| + | === Only dump a single Reference ID (<code>--refID</code>) === | ||
| + | Use <code>--refID</code> 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 (<code>--summary</code>)=== |
| − | + | Use <code>--summary</code> to print only a 1 line summary for each reference ID rather than the full output. | |
| + | |||
| + | {{paramsParameter}} | ||
| + | |||
| + | {{PhoneHomeParameters}} | ||
= Return Value = | = Return Value = | ||
* 0: the BAM index file was processed successfully. | * 0: the BAM index file was processed successfully. | ||
* non-0: the BAM index file was not processed successfully. | * non-0: the BAM index file was not processed successfully. | ||
Latest revision as of 18:01, 6 January 2014
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,
--phoneHomeThinningis 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
--noPhoneHomeis set.
Return Value
- 0: the BAM index file was processed successfully.
- non-0: the BAM index file was not processed successfully.
