Merge pull request #108 from ga4gh/defaults

Clarify defaults

Author: nsheff

docs/seqcols/README.md

@@ -647,7 +647,25 @@ Qualifer | Level1? | Level2? | Notes
 passthru | as normal | same as level1 | True if the level 2 representation is the same as the level 1 representation.
 transient | as normal | not present | True if the level 2 representation is not present.
 
+##### 4.6.1 Default values for attribute qualifiers
 
+These attribute qualifiers default to false when not explicitly specified in the schema. For a given attribute, if not specified,
+
+- `collated`: defaults to `false` (local qualifier)
+- `transient`: defaults to `false`
+- `passthru`: defaults to `false`
+- `required`: defaults to `false` (consistent with JSON Schema conventions)
+
+Similarly, when the global qualifier arrays themselves are not specified in the schema, they default to empty arrays:
+- `required`: defaults to `[]` (consistent with JSON Schema conventions)
+- `ga4gh.transient`: defaults to `[]`
+- `ga4gh.passthru`: defaults to `[]`
+
+This means that an attribute is only considered to have a qualifier set to `true` if it is explicitly:
+- Set to `true` for local qualifiers (e.g., `collated: true`)
+- Included in the appropriate array for global qualifiers (e.g., listed in `ga4gh.inherent`)
+
+A non-empty `ga4gh.inherent` array MUST be provided, because an empty `inherent` array would result in an undefined level 0 digest algorithm.
 
 #### 4.7 Method of specifying attribute qualifiers