This release contains bugfixes and security related dependencies updates.
Bugfixes and minor changes
- Changed malloc call to calloc when initializing ISA-L (fixes #177),
- Fixed setting incorrect compression level after reset call when compressing with ISA-L,
- Removed "Zero bytes written" warning messages (fixes #176),
- Fixed logger message in IntelDeflater.java,
- Removed unused Intel zlib subdirectories,
- Removed
scripts/gatk-printreads-test.py
Dependencies updates
Following dependencies were updated to latest compatible versions:
- HTSJDK 2.21.1 -> 3.0.5 (fixes CVE-2022-21126)
- TestNG 7.4.0 -> 7.5.1 (fixes CVE-2022-4065)
- Intel zlib 1.2.11 -> 1.2.13 (fixes CVE-2018-25032 and CVE-2022-37434)
- gradle 5.6.0 -> 8.0.2
Known Issues
- When compressing using ISA-L library (compression levels 1, 2) outputted compressed data size can differ by small amount of bytes (up to 100) for the same input. This does not affect original uncompressed contents. Investigation of this issue is ongoing.