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BamUtil: dumpRefInfo

1,403 bytes added, 16:54, 6 January 2014
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= 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 =
--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}}
= Usage = ./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]{{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>

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