Changes

--out        : the SAM/BAM file to be written

--out        : the SAM/BAM file to be written

Optional Parameters:

Optional Parameters:

--refFile    : reference file name used to convert any bases that match the reference to '-'

--refFile    : reference file name used to convert any bases that match the reference to '='

--keepOQ    : keep the OQ tag rather than removing it.  Default is to remove it.

--keepOQ    : keep the OQ tag rather than removing it.  Default is to remove it.

--keepDups  : keep duplicates rather than removing records marked duplicate.  Default is to remove them.

--keepDups  : keep duplicates rather than removing records marked duplicate.  Default is to remove them.

--params    : print the parameter settings

--params    : print the parameter settings

</pre>

</pre>

= Usage =

= Usage =