Change booleans to enums

[david4096]

For any field where the default boolean should not be considered false, we should offer an enum that states "no value selected" or "null" that is the default. This is currently a bug that makes documents incorrect when the values aren't known, since False is assumed.

For example, improper_placement on an alignment. https://github.com/ga4gh/ga4gh-schemas/blob/master/src/main/proto/ga4gh/reads.proto#L140