0.8.11: Bugfixes and security updates

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.

Remove Log4j

• Log4j has been removed
• A few minor code cleanups

v0.8.9

Fix to move this project to Log4j v2.17.

Active work is still ongoing. Additional static analysis scans will be completed by Jan 15.

0.8.8 : Q1 2021 Update

Update ISAL and OTC Zlib libraries to latest version (Q1 2021)
Fixed 3 reproducible issues and retested out of 4 more in GKL
Updated build for Centos 7 and Current Mac.
Valgrind on limited C unit tests (passed)
Major improvements to input validation
Major updates to Error handling and propagation.
Added Negative space unit testing coverage
Regular Static Code Scanning
Good overall quality of life improvement for the software

Major library update and memory allocation updates

updated otc zlib 1.2.8 to 1.2.11
update isa-l 2.21 to 2.28
removed libz folder
updated patch for compilation optimizations
removed shacc files and reference from c++, headers and cmake list
upgraded gradle 3.2.1 to 5.6
Fix for issue #89
Defensive code for Smithwatermen memory allocations
New build.sh script for Linux

0.8.6

Check in from GATK team

0.8.5

compression code edit, potential memory leak fixed.

0.8.4

Includes the changes to optimizations for Level 2 compression.

0.8.3

Updated the Level 2 compression via new release of ISAL-2.21.

0.8.2

Bugfixes and minor changes:

• Compression memory issue fix
• Added JNI checks to unit tests
• Minor code cleanup