Adjusted resorting bounds to account for indels in mapped reads
Throwing background thread exception before returning after a blocking call
Checking expensive assert flag before computing expensive sanity checks
Using MappedFastaSequenceFile for improved reference query performance
Caching computed soft clip evidenceID
Added minScore variant calling threshold so single-read cliques can be culling before writing breakpoints to disk.
VariantCaller no longer using global perChr setting memory usage no longer an issues and perChr processing has very high IO overhead
Increased buffer size to reduce queue contention