QueryResult new constructor with ID as only argument
Soft clipping in sequence alignments properly managed
New QueryOptions constructor for initializing using a Map
AlignmentRegion class stores both alignments, coverage and chr:start-end of a region
QueryResult stored object is now a List<T> instead of T, and AlignmentRegion contains a RegionCoverage instead of a Map
New QueryResponse class
Merge branch 'feature/alignment-query' into develop
Merge branch 'develop' of github.com:opencb/java-libs into develop