Difference between revisions of "BamUtil: dumpRefInfo"
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= Overview of the <code>dumpRefInfo</code> function of <code>bamUtil</code> = | = Overview of the <code>dumpRefInfo</code> function of <code>bamUtil</code> = | ||
The <code>dumpRefInfo</code> option on the [[bamUtil]] executable prints the SAM/BAM file's reference information. | The <code>dumpRefInfo</code> option on the [[bamUtil]] executable prints the SAM/BAM file's reference information. | ||
| + | |||
| + | = Usage = | ||
| + | ./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params] | ||
= Parameters = | = Parameters = | ||
| Line 15: | Line 18: | ||
--params : print the parameter settings | --params : print the parameter settings | ||
</pre> | </pre> | ||
| + | {{PhoneHomeParamDesc}} | ||
| + | |||
| + | == Required Parameters == | ||
| + | {{InBAMInputFile}} | ||
| + | |||
| + | == Optional Parameters == | ||
| + | {{noeofBGZFParameter}} | ||
| + | |||
| + | === Print Number of Records for each Chromosome (<code>--printRecordRefs</code>) === | ||
| + | Use the <code>--printRecordRefs</code> option to also output each reference/chromsome id, name, and the number of records with that id/name in the SAM/BAM file. | ||
| + | Example: | ||
| + | <pre> | ||
| + | Ref ID: 0 Ref Name: 1 NumRecs: 4 | ||
| + | </pre> | ||
| + | Ref ID: -1 indicates unmapped (Ref Name will be *) | ||
| + | |||
| + | {{paramsParameter}} | ||
| − | + | {{PhoneHomeParameters}} | |
| − | |||
= Return Value = | = Return Value = | ||
* 0: the file was processed successfully. | * 0: the file was processed successfully. | ||
* non-0: the file was not processed successfully. | * non-0: the file was not processed successfully. | ||
| + | |||
| + | =Sample Output= | ||
| + | <pre> | ||
| + | Reference Index 0; Name: 1 | ||
| + | Reference Index 1; Name: 2 | ||
| + | Reference Index 2; Name: 3 | ||
| + | Reference Index 3; Name: 4 | ||
| + | Reference Index 4; Name: 5 | ||
| + | Reference Index 5; Name: 6 | ||
| + | Reference Index 6; Name: 7 | ||
| + | Reference Index 7; Name: 8 | ||
| + | Reference Index 8; Name: 9 | ||
| + | Reference Index 9; Name: 10 | ||
| + | Reference Index 10; Name: 11 | ||
| + | Reference Index 11; Name: 12 | ||
| + | Reference Index 12; Name: 13 | ||
| + | Reference Index 13; Name: 14 | ||
| + | Reference Index 14; Name: 15 | ||
| + | Reference Index 15; Name: 16 | ||
| + | Reference Index 16; Name: 17 | ||
| + | Reference Index 17; Name: 18 | ||
| + | Reference Index 18; Name: 19 | ||
| + | Reference Index 19; Name: 20 | ||
| + | Reference Index 20; Name: 21 | ||
| + | Reference Index 21; Name: 22 | ||
| + | Reference Index 22; Name: X | ||
| + | Ref ID: 0 Ref Name: 1 NumRecs: 4 | ||
| + | Ref ID: 1 Ref Name: 2 NumRecs: 1 | ||
| + | Ref ID: 0 Ref Name: 1 NumRecs: 1 | ||
| + | Ref ID: 1 Ref Name: 2 NumRecs: 1 | ||
| + | Ref ID: 2 Ref Name: 3 NumRecs: 1 | ||
| + | Ref ID: -1 Ref Name: * NumRecs: 2 | ||
| + | </pre> | ||
Latest revision as of 17:54, 6 January 2014
Overview of the dumpRefInfo function of bamUtil
The dumpRefInfo option on the bamUtil executable prints the SAM/BAM file's reference information.
Usage
./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]
Parameters
Required Parameters:
--in : the SAM/BAM file to be read
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--printRecordRefs : print the reference information for the records in the file (grouped by reference).
--params : print the parameter settings
PhoneHome: --noPhoneHome : disable PhoneHome (default enabled) --phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)
Required Parameters
Input File (--in)
Use --in followed by your file name to specify the SAM/BAM input file.
The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.
A - is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).
| SAM/BAM/Uncompressed BAM from file | --in yourFileName
|
| SAM from stdin | --in - |
| BAM from stdin | --in -.bam |
| Uncompressed BAM from stdin | --in -.ubam |
Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the samtools implementation so pipes between our tools and samtools are supported.
Optional Parameters
Do not require BGZF EOF block (--noeof)
Use --noeof if you do not expect a trailing eof block in your bgzf file.
By default, the trailing empty block is expected and checked for.
Print Number of Records for each Chromosome (--printRecordRefs)
Use the --printRecordRefs option to also output each reference/chromsome id, name, and the number of records with that id/name in the SAM/BAM file.
Example:
Ref ID: 0 Ref Name: 1 NumRecs: 4
Ref ID: -1 indicates unmapped (Ref Name will be *)
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 file was processed successfully.
- non-0: the file was not processed successfully.
Sample Output
Reference Index 0; Name: 1 Reference Index 1; Name: 2 Reference Index 2; Name: 3 Reference Index 3; Name: 4 Reference Index 4; Name: 5 Reference Index 5; Name: 6 Reference Index 6; Name: 7 Reference Index 7; Name: 8 Reference Index 8; Name: 9 Reference Index 9; Name: 10 Reference Index 10; Name: 11 Reference Index 11; Name: 12 Reference Index 12; Name: 13 Reference Index 13; Name: 14 Reference Index 14; Name: 15 Reference Index 15; Name: 16 Reference Index 16; Name: 17 Reference Index 17; Name: 18 Reference Index 18; Name: 19 Reference Index 19; Name: 20 Reference Index 20; Name: 21 Reference Index 21; Name: 22 Reference Index 22; Name: X Ref ID: 0 Ref Name: 1 NumRecs: 4 Ref ID: 1 Ref Name: 2 NumRecs: 1 Ref ID: 0 Ref Name: 1 NumRecs: 1 Ref ID: 1 Ref Name: 2 NumRecs: 1 Ref ID: 2 Ref Name: 3 NumRecs: 1 Ref ID: -1 Ref Name: * NumRecs: 2
