Changed annotation interface to iterator streaming
Assigning evidence to a single breakpoint
Filtering calls with no support (due to support being assigned to alternative breakpoint)
Deadlock fix in maximal clique threading
Using DuplicateIterator background thread to prevent deadlock
Fixed evidence annotation score
Defensive programming against SAMFileWriter double-closing bug (htsjdk master has not yet accepted patch)
Using memory mapped reference genome instead of JVM buffering
Note: master htsjdk has not yet accepted my memory mapping support pull request
Added test case for more sensible CIPOS position
Corrected read pair sorting window size - previous window size did not account for soft clipped backward OEA
Added output ordering check to windowed sorting
Ensuring evidence weight is positive
Improved debugging QOL
Exposing soft clip margin as a command-line parameter
Accounting for GraphNode reordering due to soft clip margin
Removed defensive code that shouldn't happen in favour of failing early
Not writing VCF index when sorting