fix: issue warnings instead of errors when trying to check the header of hap files and issue error when output of transform is not provided to simphenotype #254
We were issuing errors in the .hap reader before but it turns out that there are perfectly legitimate reasons for the header to lack an extra field. For example, if a hap file only contains haplotypes (and not repeats) and we try to provide the hap file to simphenotype, which expects both haplotypes and repeats to be declared in the header.
This PR also switches on a message in simphenotype that would warn when the output of transform is not properly passed to simphenotype. Incidentally, I do this all the time 😅 It also converts the warning to an error.
We were issuing errors in the .hap reader before but it turns out that there are perfectly legitimate reasons for the header to lack an extra field. For example, if a hap file only contains haplotypes (and not repeats) and we try to provide the hap file to
simphenotype
, which expects both haplotypes and repeats to be declared in the header.This PR also switches on a message in
simphenotype
that would warn when the output oftransform
is not properly passed tosimphenotype
. Incidentally, I do this all the time 😅 It also converts the warning to an error.