2.13.0

Breaking changes:

• Removed B prefixed from ANRP ANSR ANRPQ ANSRQ fields.
  • Fields are now consistent with the GRIDSS convention that B prefixed fields are breakend fields
• #520 #542 require samtools 1.13 or later

Significant changes:

• #537 reverting back to using external aligner as the default soft clip realigner
  • Reverted due to:
    • in-process bwa causing JVM crashes on some systems.
    • In-process bwa alignments not deterministic when using more than 1 thread
  • Added --internalaligner flag.
    • Useful if the slight performance boost during the preprocessing step is more important that determinism

Minor changes:

• Added workaround for samtools/htsjdk#1584
• #520 @keiranmraine updated edirect install in Dockerfile
• #537 AnnotateInsertedSequence now respects --externalaligner command line argument
• Using fast compression for temporary files in the preprocess step
• Improved word wrapping in usage message
• #520 ensuring java.io.tmpdir exists before unpacking the JNI .so files
• #530 moved ulimit change to before set errexit so all ulimit failures will be silent
• Updated gridsstools to htslib 1.14
• Updated gridsstools docker building to match 1.14 htslib requirement
• Bump gridsstools version due to htslib version update
• #538 using htslib/htslib_static.mk instead of hard-coding htslib system libraries
• Added (non-default) ReadWeighted scoring model option