bamCoverage --filterRNAstrand doesn't respect --extendReads

[dpryan79]

From the mailing list, it turns out that bamCoverage --filterRNAstrand something will ignore --extendReads. This can be fixed by adding --Offset 1 -1, which was quite clever on the part of the person who submitted the report, but that shouldn't be needed.

There are two good fixes:

1. Add support for read extension to the filterRNAstrand class.
2. Check for --filterRNAstrand and set --Offset to [1, -1] in such cases. This has the benefit of reducing the amount of code that needs maintaining.

[dpryan79]

I'm going to go with option 2, since that decreases the overall amount of code :)

[dpryan79]

This is now implemented in develop.