Closed nrminor closed 1 month ago
Here's an answer key for a BED file that will work:
NC_045512.2 30 54 nCoV-2019_1_LEFT 1 +
NC_045512.2 1183 1205 nCoV-2019_1_RIGHT 1 -
NC_045512.2 1100 1128 nCoV-2019_2_LEFT 2 +
NC_045512.2 2244 2266 nCoV-2019_2_RIGHT 2 -
NC_045512.2 2153 2179 nCoV-2019_3_LEFT 1 +
NC_045512.2 3235 3257 nCoV-2019_3_RIGHT 1 -
NC_045512.2 3144 3166 nCoV-2019_4_LEFT 2 +
NC_045512.2 4240 4262 nCoV-2019_4_RIGHT 2 -
NC_045512.2 4167 4189 nCoV-2019_5_LEFT 1 +
NC_045512.2 5337 5359 nCoV-2019_5_RIGHT 1 -
NC_045512.2 5257 5286 nCoV-2019_6_LEFT 2 +
NC_045512.2 6358 6380 nCoV-2019_6_RIGHT 2 -
NC_045512.2 6283 6307 nCoV-2019_7_LEFT 1 +
NC_045512.2 7379 7401 nCoV-2019_7_RIGHT 1 -
NC_045512.2 7298 7328 nCoV-2019_8_LEFT 2 +
NC_045512.2 8363 8385 nCoV-2019_8_RIGHT 2 -
NC_045512.2 8253 8282 nCoV-2019_9_LEFT 1 +
NC_045512.2 9378 9400 nCoV-2019_9_RIGHT 1 -
NC_045512.2 9303 9327 nCoV-2019_10_LEFT 2 +
NC_045512.2 10429 10451 nCoV-2019_10_RIGHT 2 -
NC_045512.2 10343 10370 nCoV-2019_11_LEFT 1 +
NC_045512.2 11447 11469 nCoV-2019_11_RIGHT 1 -
NC_045512.2 11372 11394 nCoV-2019_12_LEFT 2 +
NC_045512.2 12538 12560 nCoV-2019_12_RIGHT 2 -
NC_045512.2 12450 12473 nCoV-2019_13_LEFT 1 +
NC_045512.2 13599 13621 nCoV-2019_13_RIGHT 1 -
NC_045512.2 13509 13532 nCoV-2019_14_LEFT 2 +
NC_045512.2 14619 14641 nCoV-2019_14_RIGHT 2 -
NC_045512.2 14540 14568 nCoV-2019_15_LEFT 1 +
NC_045512.2 15713 15735 nCoV-2019_15_RIGHT 1 -
NC_045512.2 15608 15634 nCoV-2019_16_LEFT 2 +
NC_045512.2 16698 16720 nCoV-2019_16_RIGHT 2 -
NC_045512.2 16624 16647 nCoV-2019_17_LEFT 1 +
NC_045512.2 17732 17754 nCoV-2019_17_RIGHT 1 -
NC_045512.2 17622 17649 nCoV-2019_18_LEFT 2 +
NC_045512.2 18684 18706 nCoV-2019_18_RIGHT 2 -
NC_045512.2 18596 18618 nCoV-2019_19_LEFT 1 +
NC_045512.2 19655 19678 nCoV-2019_19_RIGHT 1 -
NC_045512.2 19574 19604 nCoV-2019_20_LEFT 2 +
NC_045512.2 20676 20698 nCoV-2019_20_RIGHT 2 -
NC_045512.2 20553 20581 nCoV-2019_21_LEFT 1 +
NC_045512.2 21620 21642 nCoV-2019_21_RIGHT 1 -
NC_045512.2 21532 21562 nCoV-2019_22_LEFT 2 +
NC_045512.2 22590 22612 nCoV-2019_22_RIGHT 2 -
NC_045512.2 22511 22537 nCoV-2019_23_LEFT 1 +
NC_045512.2 23609 23631 nCoV-2019_23_RIGHT 1 -
NC_045512.2 23518 23544 nCoV-2019_24_LEFT 2 +
NC_045512.2 24714 24736 nCoV-2019_24_RIGHT 2 -
NC_045512.2 24633 24658 nCoV-2019_25_LEFT 1 +
NC_045512.2 25768 25790 nCoV-2019_25_RIGHT 1 -
NC_045512.2 25690 25712 nCoV-2019_26_LEFT 2 +
NC_045512.2 26835 26857 nCoV-2019_26_RIGHT 2 -
NC_045512.2 26744 26766 nCoV-2019_27_LEFT 1 +
NC_045512.2 27872 27894 nCoV-2019_27_RIGHT 1 -
NC_045512.2 27784 27808 nCoV-2019_28_LEFT 2 +
NC_045512.2 28985 29007 nCoV-2019_28_RIGHT 2 -
NC_045512.2 28677 28699 nCoV-2019_29_LEFT 1 +
NC_045512.2 29768 29790 nCoV-2019_29_RIGHT 1 -
The primer handling in the pipeline currently fails when primer start positions precede primer start positions, like in the primer BED file for the SARS-CoV-2 "MIDNIGHT" d1200 ARTIC primers:
To solve this, we'll need to add a step that scans the input BED file, finds any rows where start preceded stop, flip the two, and set the final column to "-". The script written for this step can eventually be expanded to a script that handles all primer BED file validation, which has previously been a sore spot for the pipeline.