'make_fastqs': enable R1/R2 read truncation to be specified on command line

[pjbriggs]

Updates the make_fastqs command so that R1 and/or R2 reads can be truncated without explicitly specifying the bases mask string (which was how this has been done in the past).

Bases mask can still be specified explicitly, however this PR implements new command line options --r1-length and --r2-length which the command will now use to adjust the default bases mask.

For example, if the default bases mask was y107,I10,I10,y107 but only the first 59 bases of the R1 and R2 sequences were needed, then specifying --r1-length=59 and --r2-length=59 would automatically adjust the masking to y59n48,I10,I10,y59n48 (rather than the user needing to manually work out and specify this themselves).

Note that the options are only applied for the standard and mirna protocols.

This PR close #884.