First take on vcf-style variants
Add variant search methods
Add missing import and bracket
Move calls above variants to fix build
message -> record

proto conversion fail
Replace GARead with GAAlignmentRecord
added a few more fields and comments
renamed GAAlignmentRecord and made closer to SAM
TAB => SPACEs
More comments
Merge remote-tracking branch 'upstream/master' into AlignmentRecord

Conflicts:
	src/main/resources/avro/reads.avdl
header comment to provide an overview of all objects
Update reads.avdl
1->0 based
Make referenceBases non-optional
clarified GAReadAlignment definition
camels > underscores
camels > underscores
Typo fix
callset -> callsample, add variantset

Also replaced contig with referenceSequenceName