every Read must belong to exactly one Readset
paired reads must belong to the same readset
shorten object names from GA4GH to GA
Merge pull request #13 from dglazer/read-to-readset

every Read must belong to exactly one Readset
Fix travis link
First step to fileData cleanup

- inline the headerSections field
- remove the header object, because neither sorting_order nor bam version is applicable in this format
- remove fileUri for the same reason
Create methods.avdl

Initial attempt at specifying 2 rpc definitions - read search and readset search.
add namespace
Delete extra newlines
Add missing import line
Remove readsets
add context (GA4GH links, team mission)
paired reads must belong to the same readGROUP
Merge pull request #19 from dglazer/s/GA4GH/GA

shorten object names from GA4GH to GA
Merge remote-tracking branch 'upstream/master' into filedata-move

Conflicts:
	src/main/resources/avro/ga4gh.avdl
Merge remote-tracking branch 'upstream/master' into methods
switch to GA prefix
Merge pull request #21 from cassiedoll/filedata-move

First step to fileData cleanup
Merge pull request #15 from dglazer/mated-reads

paired reads must belong to the same readgroup
Extended CIGAR; added barebone GADataSet

It is now possible to describe the entire chimeric alignment in one GARead
record. In case of a graph reference, each linear alignment could be an
alignment to a segment in the graph.