Pangolin exits with error if variant with wildcard character

[tsivaarumugam]

Hi Team,

While using a VCF file with wildcard character "*" in the allele field Spanning-or-overlapping-deletions-allele, Pangolin exits with error.

Example entry: 3 60539233 . AAAATATAT AATAT,* 550 PASS . . .

Error trace:
Traceback (most recent call last):
File "pangolin", line 8, in
sys.exit(main())
File "python3.8/site-packages/pangolin/pangolin.py", line 250, in main
scores = process_variant(lnum+i, str(variant.CHROM), int(variant.POS), variant.REF, str(variant.ALT[0]), gtf, models, args)
File "python3.8/site-packages/pangolin/pangolin.py", line 130, in process_variant
loss_neg, gain_neg = compute_score(ref_seq, alt_seq, '-', d, models)
File "python3.8/site-packages/pangolin/pangolin.py", line 30, in compute_score
ref_seq = one_hot_encode(ref_seq, strand).T
File "python3.8/site-packages/pangolin/pangolin.py", line 24, in one_hot_encode
seq = np.asarray(list(map(int, list(seq[::-1]))))
ValueError: invalid literal for int() with base 10: 'M'

[oleraj]

I have this issue as well. It would be better if this variant could be skipped rather than exiting.