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