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, 15:05, 30 September 2010
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| === Parameters === | | === Parameters === |
| <pre> | | <pre> |
− | Required Parameters:
| + | Required Parameters: |
− | --refFile : the path/name of the reference file
| + | --refFile : the reference |
− | Optional Parameters:
| + | --refName : the BAM reference Name to read (either this or refID can be specified) |
− | --refID : the reference ID to read, defaults to print all
| + | --start : inclusive 0-based start position (defaults to -1) |
− | --summary : only print a summary - 1 line per reference.
| + | Required Length Parameter (one but not both needs to be specified): |
| + | --end : exclusive 0-based end position (defaults to -1: meaning til the end of the reference) |
| + | --numBases : number of bases from start to display |
| </pre> | | </pre> |
| | | |
| === Usage === | | === Usage === |
− | ./bam readReference --refFile <referenceFilename> --start <0 based start> --end <0 based end>|--numBases <number of bases> | + | ./bam readReference --refFile <referenceFilename> --refName <reference Name>--start <0 based start> --end <0 based end>|--numBases <number of bases> |
| | | |
| === Return Value === | | === Return Value === |
| * 0: the reference file was successfully read. | | * 0: the reference file was successfully read. |
| * non-0: the reference file was not successfully read. | | * non-0: the reference file was not successfully read. |