Option to preserve MM/ML tags

[aliceedoe]

I thank you for the possibility to better map long reads to the repetitive regions, but I would be even more grateful if preserving the HiFi methylation tags was also possible... Not sure how the clipping affects this issue...

[arangrhie]

You can use the -y option. It will put them in the tags as they are in the input fastq file.

[Alicja-RNA]

Dear arangrhie,

Thank you very much for this answer. But this will not work for the clipped reads, if they will just appear as they were in FASTQ, or this option will also take care of this? For now, I just added the tag to the mapped reads and will not parse supplementary alignments.