Open m3hdad opened 4 months ago
Thanks for pointing this out it looks like Name was not previously in the output so I'll update/modify now.
Thanks @fmaguire !
In AMRFinderPlus there is an option --name
that prints out the sample names to the output.
You might wanna consider another approach (maybe specifying column name?) to cover both behavior in case users choose either options.
I updated the bug report to describe the behavior.
I have the following results from AmrFinderPlus by passing
--name
.Clearly "Protein identifier" is
NA
however when the data is processed by hamronizationNA
values are passed for specificnucleotide_field_mapping
columns such asContig id
,Start
,Stop
, etc.I was just wondering if in this line, for the if statement, there should be a clause to consider whether the user chooses to use
--name
or not as index 0 might not always reflect "Protein identifier" column.This is quite misleading when there are two copies of res genes matching with the same reference since the important information on contig id, start, stop columns will be ignored. See rows 2 and 3 in this example.