Add an id field to read alignment

This id field helps callers disambiguate between reads from different API responses. This field was in v0.1, and the 3 implementors all have it - so hopefully it should be okay to keep it around. (and it's just like all of our other object ids)
Comment cleanups to improve generated docs
Merge remote-tracking branch 'upstream/master' into doc-cleanups

Conflicts:
	src/main/resources/avro/variantmethods.avdl
	src/main/resources/avro/variants.avdl
Add missing GA prefix to variant methods
Additional comment cleanups
improve mapping quality comment
Merge remote-tracking branch 'upstream/master' into doc-cleanups

Conflicts:
	src/main/resources/avro/reads.avdl
Rename start/endPosition to start/end
Merge pull request #95 from cassiedoll/doc-cleanups

Comment cleanups to improve generated docs
Merge remote-tracking branch 'upstream/master' into start-end

Conflicts:
	src/main/resources/avro/readmethods.avdl
Merge remote-tracking branch 'upstream/master' into add-missing-prefixes

Conflicts:
	src/main/resources/avro/variantmethods.avdl
Merge pull request #102 from cassiedoll/start-end

Rename start/endPosition to start/end
Merge pull request #98 from cassiedoll/add-missing-prefixes

Add missing GA prefix to variant methods
Rename ReferenceSequence* -> Reference*
Merge pull request #96 from cassiedoll/reference-rena

Rename ReferenceSequence* -> Reference*