brentp/bpbio

basepair bio: a single binary with many useful genomics subtools.

bpbio's Issues

variexpr: support modes other than trio

currently, variexpr works quite nicely for trios, but it does not have a mode for iterating over each sample. this might be out of scope or might require a cohort mode that is separate from trio mode.

variexpr: affected, unaffecteds

• should be able to check sample.affected and sample.unaffected.where affected is a boolean
• add affecteds = seq[Sample] and unaffecteds = seq[Sample] for any .ped file with any affected samples. Then user can write a function to iterator over these and return a boolean or number (yet to support numeric returns).

if duktape supported "fat arrow" functions, this would have a nice API. For now, it will have to do that the user runs a function, iterates over each affected or unaffected and returns a result.

variexpr: things to add

• : variant object with CHROM, POS, start, end, REF, ALTS, QUAL, ID, FILTER
• : variant.call_rate
• : variant.hwe
• : variant.num_hets, variant.num_hom_ref, variant.num_unknown, variant.num_hom_alt

add access to CSQs

INFO.CSQ will be the original string.

CSQS will be the list of all CSQS
CSQ will be the "highest" impact.

should have CSQ.gene, CSQ.symbol, CSQ.transcript, in addition to whatever is in the Description upon annotation.

variexpr: support returning a number

currently, only boolean expressions are supported. need to determine how to support a numeric return value. this is easy to implement, but making it nice for the user is harder.