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, 18:07, 6 January 2014
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| = Overview of the <code>readReference</code> function of <code>bamUtil</code> = | | = Overview of the <code>readReference</code> function of <code>bamUtil</code> = |
| The <code>readReference</code> option on the [[bamUtil]] executable prints the specified region of the reference sequence in an easy to read format. | | The <code>readReference</code> option on the [[bamUtil]] executable prints the specified region of the reference sequence in an easy to read format. |
| + | |
| + | = Usage = |
| + | ./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params] |
| | | |
| = Parameters = | | = Parameters = |
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| --numBases : number of bases from start to display | | --numBases : number of bases from start to display |
| </pre> | | </pre> |
| + | {{PhoneHomeParamDesc}} |
| | | |
− | = Usage = | + | == Required Parameters == |
− | ./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
| + | {{RefFile}} |
| + | |
| + | === Reference Name (<code>--refName</code>) === |
| + | The Reference/Chromosome Name to read from the reference file. |
| + | |
| + | === Start Position (<code>--start</code>) === |
| + | Use <code>--start</code> to specify the 0-based position to start printing bases from. |
| + | |
| + | === Length Parameters (<code>--end</code>, <code>--numBases</code>) === |
| + | The length of the reference to be printed must be specified. |
| + | |
| + | Use <code>--end</code> to indicate the exclusive 0-based end position. |
| + | |
| + | :OR (but not both) |
| + | |
| + | Use <code>--numBases</code> to indicate the number of bases to display. |
| + | |
| + | {{paramsParameter}} |
| + | |
| + | {{PhoneHomeParameters}} |
| | | |
| = Return Value = | | = Return Value = |