Fixes #2016 (closed).
The merge request doesn't include any documentation change, which could look weird. However I think this should remain a hidden feature for two reasons:
- A BAM file is generally obtained by aligning reads to reference sequences. This could make people think they have to align their reads beforehand.
- In the case of paired-end sequencing, there is only one BAM file (but two FASTQ files). So the people could provide a single BAM file where reads have not been merged.