Fix to sam->bam conversion step.

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:

```python
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.