Currently, there are two issues with pseudocigar handling in create_representative_microhaplotype_dict()
- It currently stores pseudocigar as pseudo_cigar, which is not the proper name in the schema (should be pseudocigar)
- pseudocigar should be a class of pseudocigar with values for the pseudocigar itself, but also the reference location that the pseudocigar refers to, as this will change how to interpret the pseudocigar
Attempted to fix by change
if val := get_if_present(row, pseudocigar_col):
mhap["pseudo_cigar"] = val
to
if val := get_if_present(row, pseudocigar_col):
mhap["pseudocigar"] = val
but this goes agains the schema where this should be a object that looks like
"pseudocigar" : {
"pseudocigar_seq" : "8M",
"ref_loc" :
{
"chrom" : "Pf3D7_01_v3",
"end" : 145621,
"genome_id" : 0,
"start" : 145448,
"strand" : "+"
}
}
rather than
Currently, there are two issues with pseudocigar handling in create_representative_microhaplotype_dict()
Attempted to fix by change
to
but this goes agains the schema where this should be a object that looks like
rather than