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, 17:54, 6 January 2014
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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 = |
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| --params : print the parameter settings | | --params : print the parameter settings |
| </pre> | | </pre> |
| + | {{PhoneHomeParamDesc}} |
| | | |
| + | == Required Parameters == |
| + | {{InBAMInputFile}} |
| | | |
− | printRecordRefs outputs the id, the name, and the number of records with that id/name in the SAM/BAM file. | + | == 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: | | Example: |
| <pre> | | <pre> |
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| Ref ID: -1 indicates unmapped (Ref Name will be *) | | Ref ID: -1 indicates unmapped (Ref Name will be *) |
| | | |
− | = Usage =
| + | {{paramsParameter}} |
− | ./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]
| + | |
| + | {{PhoneHomeParameters}} |
| | | |
| = Return Value = | | = Return Value = |