modification support for DORADO

[lpryszcz]

Hi Luca, mostly copy-paste from @soniacruciani with some of my comments:

dorado encodes modifications (ie when using RNA004 m6A DRACH model) in bam files (MM and ML tags).
In order to support dorado m6A model in the upcoming release we have two options:

1. do mapping via dorado - BAM output is already mapped. this is not ideal because dorado doesn't support much control over alignement ie lack of spliced alignment.
2. do mapping after basecalling and include modification info (MM and ML tags) in FastQ and BAM using following commands

dorado basecall > unmapped.BAM_with_mods_from_dorado
samtools view -F3840 -bu unmapped.BAM_with_mods_from_dorado | samtools fastq -T MM,ML,mv,pt,ts > fastq_with_mods
minimap2 -y ... $ref fastq_with_mods | samtools sort --write-index -o mapped.BAM.with_mods

Note, the second option is troublesome, because dorado/remora uses reference sequence in order to make better modification calls (reference-anchored calling). So if we go for it, expect lower modification calling accuracy.

If we go for 2nd option, I'd recommend to include a few more useful tags in final BAM:

• mv - move table
• pt - estimated polyA tail length
• ts - template start