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tianwen0003 avatar tianwen0003 commented on July 29, 2024

I found this error is caused because the function group_reads_by_snps invoked by the function read_pair_combos did not merge the candidate variants-overlapped-read1 to one set appropriately, instead put them in seperate sets. I add follwing code between line 821 and line 822 of the find_intersecting_snps.py

if len(new_reads[0]) > 1:
    original_new_reads_0 = new_reads[0]
    justed_new_reads_0 = set()
    for i in original_new_reads_0:
        for j in i:
            justed_new_reads_0.add(j)
    justed_new_reads_0 = [justed_new_reads_0]
    new_reads[0] = justed_new_reads_0

if len(new_reads[1]) > 1:
    original_new_reads_1 = new_reads[1]
    justed_new_reads_1 = set()
    for i in original_new_reads_1:
        for j in i:
            justed_new_reads_1.add(j)
    justed_new_reads_1 = [justed_new_reads_1]
    new_reads[1] = justed_new_reads_1

from wasp.

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