Ideas

Make a tool for indexing FASTA, or at least reusing index created by samtools

There will be a need to fetch regions from reference sequence, at least for pileup. However, this is not so important nowadays, as many BAM files come with MD tags filled. Alternatively, most reference sequences can be loaded directly into memory due to their relatively small size.

SNP caller

I have started porting Samtools caller to BioD, but the work is not finished (only mismatches are called). See BioD/bio/bam/snpcallers/maq.d

Sliding window support

Rather than feed BED files in many cases 'programmed' sliding window support would be really useful (Joep de Ligt)