Bug fix release. Includes update to latest version of log4j
- Updated log4j transitive dependency to 2.17.1. Log4j is only used in the command-line parsing library
- Ignoring unmapped primary records when supplementary alignments exist
- supplementary record will treated as the primary alignment
- #560 removing any left-over .sv.tmp.bam files
- Improved determinism
- Removed unnecessary samtools merge munging of RG/PG headers
- Forcing deterministic ordering when merging SAM records from multiple input files