BAM as input?

[jfy133]

Is your feature request related to a problem? Please describe.
Sometimes we receive/download only BAM files (e.g. see Slon et al. 2017 data on ENA), that we wish remap/reprocess in a different context. For example if the data is metagenomic, and we want to map to a particular bacterial genome. Currently we would have to manually re-convert the BAM to FASTQ, which leads to unnecessary data redundancy.

Describe the solution you'd like
An option to provide BAM as an input, rather than FASTQ. One solution would with a -bam flag, which would (turn-off a clip/merge module? and then) pipe stdout from samtools fastq into the mapper itself.

Describe alternatives you've considered
One could just manually re-convert the BAM.

[apeltzer]

Yup, that sounds good! I guess having a step to run on BAM directly would be quite easy to establish...

[jfy133]

This may also require a skip adapter_removal step of some kind, in case you want to re-run already preprocessed data.

[apeltzer]

This is addressed in #129