Only provide BAM output

[armintoepfer]

Drop all output files except for BAM. Annotate metrics to each record using custom BAM tags, such as super-read coverage or the read names of that were used.

[tobiasmarschall]

I agree to make BAM the default output. Having some optional "side output" such as FASTA might still be helpful.

[armintoepfer]

In my opinion, we can rather provide samtools one-liners to extract certain information in a different format.

[tobiasmarschall]

Also makes a lot of sense. That is, if we generated the according documentation.