Cleanup of temporary SAM and BAM files

Cleans up the temporary SAM and BAM files in the `mapping/` and `sam/` directory (for issue #9 ).  Removes the majority of the unneded files being stored.  For example

original `du -s *`
```
288114  output_original/mapping
84666   output_original/sam
63106   output_original/bam
44354   output_original/mpileup
```
new `du -s *`
```
63106   output_new/bam
44354   output_new/mpileup
...
474     output_new/mapping
...
2       output_new/sam
```

Any other files we should be cleaning up (I still like keeping around one copy of the BAM files)?