BamUtil: dumpRefInfo: Difference between revisions
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--params : print the parameter settings | --params : print the parameter settings | ||
</pre> | </pre> | ||
printRecordRefs outputs the id, the 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 *) | |||
= Usage = | = Usage = | ||
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* 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> | |||
Revision as of 10:34, 29 September 2011
Overview of the dumpRefInfo function of bamUtil
The dumpRefInfo option on the bamUtil executable prints the SAM/BAM file's reference information.
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
printRecordRefs outputs the id, the 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 *)
Usage
./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]
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
