CRISPRessoBatch in HDR mode not accepting multiple qwc values

[alexandyan]

When specifying both amplicon_seq and expected_hdr_amplicon_seq values in CRISPRessoBatch, multiple qwc values are not accepted.

Runs properly:
CRISPRessoBatch --batch_settings batch4.tsv -qwc 5-10

CRISPRessoBatch --batch_settings batch4.tsv -qwc 5-10,5-10
returns the error:
File "/miniconda3/envs/crispresso2_env/lib/python3.12/site-packages/CRISPResso2/CRISPRessoBatchCORE.py", line 272, in main
curr_amplicon_quant_window_coordinates_arr[idx] = coords
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
IndexError: list assignment index out of range

[Colelyman]

Hi @alexandyan,

Thanks for using CRISPResso! This may or may not be a bug, depending on what you are intending to do. For the -qwc parameter, the , will delimit the QWC between amplicons, while the _ will allow you to specify multiple ranges for a single amplicon.

Using your example, are you hoping to have 5-10 apply to the reference amplicon_seq and then have a different QWC apply to the expected_hdr_amplicon_seq? If you would like the same QWC to be applied to multiple amplicons, you can just specify a single one and it will be applied to all of your amplicons.

Let us know if there is still undesired behavior, or you have any more issues. If you want to see exactly what the QWC's are for the runs, you can use this script. https://gist.github.com/Colelyman/24f1f89d1bee44c45a071e0da0b6144c

Thanks,
Cole