minimap2 module: retain ML:B tag about alignparse HOT 3 CLOSED

I'm not completely certain I recommend alignparse as a general purpose way to run minimap2. But I can see where it might be useful. If you want me to do this, can you create and post a short example including the commands you are. using and a small data file with the tags you want to keep.

from alignparse.

Hi,
I've actually found out that the -y option of minimap2 is suitable for my needs, because it retains the tags that I need, so I ended up not using alignparse for my analyses. Before, I realized this I had been playing around a little with the code to try and implement retaining tags of the B-type, I will try to create pull-request to show what I had tried (I am not very experienced so I apologize if I make a mistake).
I have attached a small subset of the reads that contain the MM and ML tags that I'm interested in.

The commands I used were:

test_ref_file = '/home/cdebuck/ref.fasta'
test_fastq = '/home/cdebuck/sample_fastq.txt'
out_sam_file = '/home/cdebuck/test/alignparse_test_minimap.sam'
options = ['-ax', 'map-ont', '-t 16']
retain_tags = ['MM', 'ML']
mapper = minimap2.Mapper(options, check_cs=False, retain_tags=retain_tags)
mapper.map_to_sam(test_ref_file, test_fastq, out_sam_file)

sample_fastq.txt

from alignparse.

Great, thanks. I'm closing this issue then.

from alignparse.