View source for BamUtil: dumpRefInfo

[[Category:BamUtil|dumpRefInfo]]
[[Category:BAM Software]]
[[Category:Software]]

= 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.

= Usage =
 ./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]

= Parameters =
<pre>
    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
</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 =
*     0: the file was 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>