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?
It depends on how long your contigs/chromosomes are. The biggest benefit to CSI is that it supports indexing BAM files with contigs longer than 2^29-1 bases. At least in plants this isn't an uncommon requirement.