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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}} |
| + | |
| + | == 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 =
| + | {{PhoneHomeParameters}} |
− | ./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]
| |
| | | |
| = 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> |