Missing required input fields about detin HOT 3 CLOSED

Hey Erle,

Sorry for the errors I will add your headers and fix the wiki to reflect the code. For clarification Num_Targets is the correct equivalent to n_probes. I just pushed a fix that removes the requirement for the ref sum and alt sum columns and will automatically fix the header for the seg file.

Thanks for pointing these out!

Best
Amaro

from detin.

Hi, I was getting stuck on the same problem, as I read in the "Description of inputs" page on the wiki, those columns shouldn't be required, and I got the impression that they aren't used in the code at all.

I eddited one line at the "read_call_stats_file" funtion on deTiN/deTiN.py as bellow:
def read_call_stats_file(self):
# on 'fields' I remove several field requirements
# they weren't on wiki's "Description of inputs" and apparently weren't actually being used.
fields = ['contig', 'position',
't_alt_count', 't_ref_count' , 'n_alt_count', 'n_ref_count', 'failure_reasons', 'judgement']
#... continues as normal

It appears to fix those problems for good.

from detin.

Hi it seems like from the most recent version you just removed the alt/ref alleles and tumor and normal sample names? You're right these aren't required by deTiN so that should work just fine. I just include them because they are useful later on.

fields = ['contig', 'position', 'ref_allele', 'alt_allele', 'tumor_name', 'normal_name', 't_alt_count',
't_ref_count'
, 'n_alt_count', 'n_ref_count', 'failure_reasons', 'judgement']

from detin.