Is there a tool to convert soft clipping to hard clipping in bam files?

Question

[Ryan Thompson]

My lab is developing a pipeline to analyze some paired-end methyl-seq data. One of the steps is to soft-clip overlaps between read pairs to prevent downstream tools from double-counting the overlapped region, using bamutil clipOverlap (http://genome.sph.umich.edu/wiki/BamUtil:_clipOverlap). However, one of the downstream tools, methylKit, will not accept soft-clipped reads, so I would like to convert the soft clipping to hard clipping in order to input it into methylKit. Is there a tool for converting soft clipping into hard clipping? Or is the conversion simple enough to implement myself?

[Devon Ryan]

FYI, PileOMeth has a --methylKit option that will create methlyKit-compatible output and not require you to do any mucking around with artificially hard/soft clipping bases. Perhaps that already does what you need.