problem with sequence corrector

[irinatu]

I have Error message that I do not understand completely. Could you help me, please?

Running SequenceCorrector at 2022-11-03 11:25:43 . . .

ERROR: Component "SequenceCorrector" failed, giving the following error message:==============================================================
Traceback (most recent call last):
File "/home/irina/bin/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/make_variant.py", line 430, in
merged_variants)
File "/home/irina/bin/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/make_variant.py", line 325, in correct_sequence
raise RuntimeError(s)
RuntimeError: Error: Unable to determine variant sequence. Conflicting (overlapping) variant sequences present.

[Psirving]

I'm not entirely certain, but I think this means that SequenceCorrector is detecting multiple variants and that they are too different to merge into a single "correct" sequence. For example, if there were two alleles that are multiple SNPs away from the provided fasta in different directions, it might produce this error.

[irinatu]

Thank you for a prompt reply. Best regards, Irina. From: Patrick Irving ***@***.***> Date: Thursday, 3 November 2022 at 17:15 To: Weeks-UNC/shapemapper2 ***@***.***> Cc: irinatu ***@***.***>, Author ***@***.***> Subject: Re: [Weeks-UNC/shapemapper2] problem with sequence corrector (Issue #37) I'm not entirely certain, but I think this means that SequenceCorrector is detecting multiple variants and that they are too different to merge into a single "correct" sequence. For example, if there were two alleles that are multiple SNPs away from the provided fasta in different directions, it might produce this error. — Reply to this email directly, view it on GitHub<#37 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADCWFTKRHVVSXYXV5CPA6UDWGPQJHANCNFSM6AAAAAARV7RFFI>. You are receiving this because you authored the thread.Message ID: ***@***.***>