Options to set scoring manually

[mbhall88]

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Dorado subcommand

Demux

Feature request

I would really like some command line options to manually set the scoring options for demultiplexing.

I know I can use the custom arrangement files, but these are frustrating if I just want to change the scoring for an existing barcode kit as I then have to go and hunt down the mask_front, mask_rear, barcode pattern etc. in the code.

[mbhall88]

This might be a separate issue, but I have been trying to adjust the max_barcode_penalty for a run that used the RBK114-96 kit. I have dropped the penalty to 3, but I still get the exact same classifications as the default. What am I doing wrong here?

[arrangement]
name = "RBK096_kit14"
kit = "BC"
mask1_front = "GCTTGGGTGTTTAACC"
mask1_rear = "GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA"

# Barcode sequences
barcode1_pattern = "BC%02i"
first_index = 1
last_index = 96
rear_only_barcodes = false

## Scoring options
[scoring]
max_barcode_penalty = 3
barcode_end_proximity = 75
min_barcode_penalty_dist = 3
min_separation_only_dist = 6
flank_left_pad = 5
flank_right_pad = 10
front_barcode_window = 175
rear_barcode_window = 175
midstrand_flank_score = 0.9

[malton-ont]

@mbhall88,

Thanks for the feature request - we'll discuss it in the team.

Regarding your classification issue, please provide your full command line and the output when using the -v flag. This may be better as a separate ticket.