allow some X hets in males, denovo imprinted, exome only CNV false po…

[RuthEberhardt]

…s inheritence in singletons

A couple of changes I was working on last year:
1 - allow some SNPs in male X which are called as hets - those which are denovos or have variant allele fraction >0.8 are kept and are treated as homs for the clinical filtering
2 - allow denovo variants on imprinted genes through

A more recent change:
3 - exome only CNVs fail if cifer prediction is false positive, which is fine for trios but in singletons the majority of cifer predictions are false positive, so this prevents exome only CNVs from singletons coming through clinical filtering. So disabling this filter in non-trios for now

[coveralls]

Coverage increased (+0.04%) to 87.518% when pulling 347cf57 on RuthEberhardt:master into 844e85b on jeremymcrae:master.

[jeremymcrae]

Do you want me to check over this, or just merge it in? I haven't substantially looked at this code since 2017, so you've got a better idea about what's needed. I think you've got push rights to this repo, so you could even merge it in yourself, if you prefer.