run_sam2cov option request

[e-manduchi]

In some cases the gene model files one uses for their analyses have chromosomes simply denoted as 1, 2,...X, Y instead of chr1, chr2, ..., chrX, chrY. I've run into this problem with SusScrofa 10.2 gene models gotten from ENSEMBL. The consequence of this is that the cov plots generated by the pipeline also have chromosomes denoted without the prepended 'chr'. Unfortunately this causes a problem when one then tries to load such coverage plots on the UCSC genome browser. They lead to a non-enlightening browser error such as:
'unrecognized type=bedGraph on line 2 of file somefile.gz'.
Prepending 'chr' to the first column of these files, fixes the problem.
Would it be possible to add an option to this script that will prepend 'chr' to all non-header values in the first column of the coverage plot files generated?

[e-manduchi]

Note that the same request applies to the junction files