Discrepancy between "query_end" value in "ChainAlignment" and the length of the output sequence

[abualrou]

ANARCI displays an inconsistency in some cases between the query_end value from the ChainAlignment and the length of the generated output sequence.

Example:

input_seq = 'AQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNQAGTALIFGKGTTLSVSSNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFN'

Result:

• anarci_output_seq = 'AQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNQAGTALIFGKGTTLSVSS'

• query_end = 111

When the query_end value is used to slice the input_seq, the resulting sequence does not match the anarci_output_seq. For instance, input_seq[0:query_end] produces 'AQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNQAGTALIFGKGTTLSVS', which is not the same as the expected anarci_output_seq.

[jackdent]

I observe similar behaviour with the following input:

sequence='EVQLVESGGDLVKPGGSLKLSCAASGFSFSSYGMSWVRQTPDKRLEWVATISNGGGYTYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDSAMYYCARRERYDENGFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR'

query_start=0
query_end=119 
query_seq='EVQLVESGGDLVKPGGSLKLSCAASGFSFSSYGMSWVRQTPDKRLEWVATISNGGGYTYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDSAMYYCARRERYDENGFAYWGQGTLVTVS'

fv_seq='EVQLVESGGDLVKPGGSLKLSCAASGFSFSSYGMSWVRQTPDKRLEWVATISNGGGYTYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDSAMYYCARRERYDENGFAYWGQGTLVTVSA'