Initial check-in, just putting the classes somewhere without much change to the interface
MANTA-17 Adopting assembler interface to manta
Renaming SmallAssembler
MANTA-17: Changing SVLocusAssembler to use new bam streamer interface
MANTA-17 Adding dummy test for semi-alignedness
Merge branch 'master' into MANTA-17
MANTA-17: Finishing integration of SVLocusAssembler
MANTA-17 Adding check for semi-alignedness to sv locus scanner
MANTA-17 Adding (draft of) module to call/test SVLocusAssembler
MANTA-17 intermediate commit
MANTA-17 Add stupid workaroung to linker dependencies
MANTA-17 Finished command line app
MANTA-17 Finishing SVLocusAssembler testing app
wqMerge branch 'master' into MANTA-17
reorder libraries to reflect library dependency chain
MANTA-17 Renaming SVCandidateDataGroup => SVCandidateReadPairGroup
Merge branch 'master' into MANTA-17
MANTA-17 Adding logic to attached contigs and their alignments to SVCandidate
demonstration function which grabs the reference for each breakend region +/-100 bases
MANTA-17 Aligning contigs using JumpAligner, storing alignment results in SVCandidateData