Fix to sam->bam conversion step.

[roryk]

I think this was bugged, it looks like bake doesn't move positional arguments to the end when the command is baked, and samtools expects the "-" to be at the end:

sh.samtools.view("-", b=True, S=True, u=True)

runs it like this:

samtools view - -b -S -u

which doesn't work. You can bake the keywords then bake the positional arguments after and that works though.

[chapmanb]

Thanks Rory. It's strange I didn't run into the positional requirement, maybe it is dependent on the samtools version.