For contributions
see
[contributors](https://github.com/freebayes/freebayes/graphs/contributors)
and
[commits](https://github.com/freebayes/freebayes/commits/master).

## ChangeLog v1.3.9 (20250215)

This is a maintenance release of Freebayes:

+ again fixes for Debian and Ubuntu
+ github actions should clear with newer vcflib
+ try cleaner meson build on Debian
+ A recent version of vcflib installs include files in include/vcflib. freebayes breaks with older vcflib.
+ Removed unused GenotypePriors.cpp, alleles.cpp, dummy.cpp

## ChangeLog v1.3.8 (20240423)

This is a maintenance release of Freebayes:

+ fixes for Debian https://github.com/freebayes/freebayes/issues/786, thanks Hrithik Mangla and Nilesh Patra for reporting
+ unbundled vcflib and vendored back in the much smaller fastahack and smithwaterman modules until Debian provides the include files

Note:

+ quality scores in test/regression/NA12878.chr22.tiny.vcf changed with recent builds. Probably caused by gcc-13 and we should look into that
+ github-CI won't build until wfa2lib is included from Debian (WIP)

## ChangeLog v1.3.7 (20230212)

+ sanitizing git submodules
+ skip bed comment lines (thanks @jodyphelan)
+ tweaks to improve performance on long reads
+ Updated intervaltree module so build passed with gcc-11.
+ Remarks and stub for `HTSCODECS_VERSION_TEXT`

## ChangeLog v1.3.6 (20220121)

This is a maintenance release of Freebayes:

+ Added parallel snakemake example and text (thanks @sanjaynagi)
+ Updated packaged htslib build to release 1.14
+ README fixes https://github.com/freebayes/freebayes/issues/726 (thanks @veghp)
+ Add option to force use of submodule deps (thanks @jnumm)
+ Using recent guix shell support for building freebayes
+ Added static build support with meson+ninja
+ Started tracking freebayes performance in ./test/performance/benchmark.md
+ Added matrix channel badge to README
+ Added Pjotr Prins as maintainer in README and banner

The provided static binary is built against gcc 10.3.0 and htslib 1.12.

Note that at this point the static binary builds with:

    meson build -Dstatic=true -Dprefer_system_deps=false --buildtype release

## ChangeLog v1.3.5 (20210210)

This is a maintenance and bug-fix release of Freebayes:

+ Namespace Fasta* classes which has a build conflict with fastahack
  https://github.com/freebayes/freebayes/commit/00594a1db84855f99c9fe2c23305b86fa542dff2
  (thanks @jnumm)

## ChangeLog v1.3.4 (20210129)

This is a maintenance and bug-fix release of Freebayes:

+ 9 issues [closed](https://github.com/freebayes/freebayes/milestone/1?closed=1)
+ Added support for --trim-complex-tail with #139 and 97735089a1bbf658862fb16f4514c0ad93195e0a (thanks @tsibley)
+ Fixed meson to not build dependencies if they are found to be installed. This should facilitate Debian builds (thanks @jnumm)
+ Cleanup and small fixes (thanks @jnumm)
+ Tested running combinations of builds with installed libs and local builds (htslib, vcflib, tabixpp --- only seqlib needs confirmation)
+ Updated scripts to use python3 (thanks @tillea)

## ChangeLog v1.3.3 (20201213)

This is a maintenance release of Freebayes:

+ Freebayes compiles for ARM64
+ Freebayes supports CRAM and we added a test for CRAM and a hint in
  the README
+ Added Meson+Ninja build system for faster builds
+ Merged: Set CRAM reference for the reader #632 (thanks @SebastianHollizeck)
+ Merged: Fix help messages for python tools #635 (thanks @ibebio)
+ Fixed: Please port to Python3 #569 which removes Debian patch (thanks @tillea)
+ Moved unused files from ./src to ./contrib/freebayes
+ Moved stripped SeqLib source into ./contrib/SeqLib as SeqLib is no
  longer maintained
+ Made htslib a primary dependency of freebayes
+ Updated htslib to the latest version
+ Fixed clang build, requires a patch on htslib sent upstream with https://github.com/samtools/htslib/pull/1190
+ Applied https://github.com/walaj/SeqLib/pull/53 (thanks @jmarshall)
+ Freebayes builds against stock htslib for Debian etc. Unfortunately
  Debian does not include htslib headers, nor does it handle LZMA
  codecs for CRAM, so the source tree is pulled in for local
  builds. See #664.
+ Updated travis-CI: passes new meson builds for gcc
+ Added github-CI: passes

Some minor stuff:

+ Added regression test so we track some changes through git repo
+ Added github agent to deal with stale issues on the issue tracker

## Earlier release notes

See github [releases](https://github.com/freebayes/freebayes/releases)