I get an error using `contains`: set element type: ‘struct{locus: locus}’ type of arg ‘item’: ‘locus’

Hail Query & hailctl
1

I tried option number 2 but got the following error after the second line:

mt = mt.filter_rows(variants_to_include_set.contains(mt.locus))

TypeError: ‘SetExpression.contains’ expects ‘item’ to be the same type as its elements
set element type: ‘struct{locus: locus}’
type of arg ‘item’: ‘locus’

Any idea what I’m doing wrong?

2

Hey @Mark,

Sorry you’re running into this problem.

This is because there is a difference between a struct containing a locus:

hl.struct(locus=hl.locus(...))

and a locus:

hl.locus(...)

You can fix this with:

mt = mt.filter_rows(variants_to_include_set.contains(hl.struct(locus=mt.locus)))

Alternatively, you can create a set that doesn’t have the unnecessary struct wrapper. Tim’s example in the other thread would look like this:

variants_to_include_set = hl.literal(set(variants_to_include.key.locus.collect()))
3

Gotcha. Thanks! I couldn’t figure out how to get rid of the structure wrapper.

4

For completeness, let me note that you can also fix the set itself.

Any set or array that contains structs can “project” one field of the struct like this:

variants_to_include_set = variants_to_include_set.locus

You could also use map:

variants_to_include_set = variants_to_include_set.map(
    lambda a_struct: a_struct.locus)