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
- Fields are now consistent with the GRIDSS convention that
- #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
- Reverted due to:
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