Dear lazyweb, here is the new menu for `samtools index`:

```
Usage: samtools index [-bc] [-m INT]  [out.index]
Options:
  -b       Generate BAI-format index for BAM files [default]
  -c       Generate CSI-format index for BAM files
  -m INT   Set minimum interval size for CSI indices to 2^INT [14]
```

What is the **CSI** index compared to **BAI**? Should I better use it instead of the 'old' BAI index? What's the benefit?
CSI also allows to choose a compromise between the size of index and region query performance (the `-m` parameter). The less the interval size, the larger the index is, but for region queries less computational work is required, because the index is more fine-grained.

BAI is a special case of CSI, with some minor differences.