apetkau/core-phylogenomics — pull request #10 by apetkau (2014-10-30 13:55:42+00:00)
Title: 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)?