Closed zihhuafang closed 3 years ago
@zihhuafang I was able to reproduce this. Looks like it can return a list of byte arrays on https://github.com/Illumina/BeadArrayFiles/blob/develop/module/GenotypeCalls.py#L399 vs. a list of strings from https://github.com/Illumina/BeadArrayFiles/blob/dc4eb370fa97582db3857680cbf3071cde9a6ec5/module/GenotypeCalls.py#L307
For a quick fix, I think you can just cast top genotypes to a string when you write it. i.e. str(top_strand_genotype)
in your example.
@jjzieve Thanks a lot for the quick fix. I ended up with str(top_strand_genotype,'UTF-8')
to print the genotypes without b'XX'.
Thanks again!
Hi thanks for providing this python library for array genotype calling.
I wanted to include top_strand genotypes as a part of the final report by including
top_strand_genotypes = gtc.get_base_calls()
in the gtc_final_report.py as shown below.However, I encountered the issue below.
When I removed the parts related to top_strand_genotype, the script worked. I am not sure what went wrong and how to modify it. If someone has experience to call TOP genotypes, I would appreciate your input on this matter.
Thanks in advance. Zih-Hua