Inconsistent knowledge for DPB1*01:01:01 about imgthla HOT 4 CLOSED

Can you please confirm the alleles and branch the files are found in. The latest release has two alleles matching DPB101:01:01 (DPB101:01:01:01 and DPB1*01:01:01:02) and the alignment file is now named DPB1_nuc.txt. Reviewing these files the DPB1_nuc.txt and DPB1_nuc.fasta appear consistent for these alleles.

from imgthla.

My apologies, I meant allele DPB1*13:01:02. I erred in my copy-and-pasting. Yes, I'm using DPB1*01:01:01:01 as the reference allele. The difference is between the DPB1_nuc.txt or DPB1_nuc.fasta files.

For example, the last part of the alignment file for the reference and the allele:

$ grep -E "DPB1*01:01:01:01|DPB1*13:01:02" alignments/DPB1_nuc.txt | tail -n 2
DPB101:01:01:01 AAG AAA G|TT CAA CGA GGA TCT GCA TAA
DPB113:01:02 --- --- -|-- --- --- --- --- --- --*

Sorry, but the font sizes won't line up. The last line of DPB1*13:01:02's fasta entry:

$ gawk 'BEGIN { RS=">" }; /DPB1*13:01:02/{printf RS; printf $0}' fasta/DPB1_nuc.fasta | tail -n 1
GGAGTGGGCATCTTCATGCACAGGAGGAGCAAGAAAGTTCAACGAGGATCTGCATAA

from imgthla.

We are currently looking to see if this discrepancy is in any of the other formats. Once this is compete, we will look at applying an update to the necessary files.

from imgthla.

This should be addressed in the latest release (3.31.0)

from imgthla.