Debian test release

v1.3.8-pre3

Put Variant.h as vcflib/Variant.h

freebayes 1.3.8

ChangeLog v1.3.8 (20240423)

This is a maintenance release of Freebayes:

• fixes for Debian #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)

freebayes 1.3.7

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

freebayes 1.3.6

This is a maintenance release of Freebayes. The provided binary is quite a bit faster (see benchmark):

• Added parallel snakemake example and text (thanks @sanjaynagi)
• Updated packaged htslib build to release 1.14
• README fixes #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

freebayes 1.3.5

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
  00594a1
  (thanks @jnumm)

If you want the executable binary use v1.3.4 below - it is the same.

freebayes 1.3.4

ChangeLog v1.3.4 (20210129)

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

• 9 issues closed
• Added support for --trim-complex-tail with #139 and 9773508 (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)

freebayes 1.3.3

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 samtools/htslib#1190
• Applied walaj/SeqLib#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

python3

This ensures python3 compatibility, but is otherwise very similar to v1.3.1.

Depth skipping bugfixes

This is a point release over v1.3.0 that includes some important fixes to make the depth skipping work correctly. It also includes a fix for a "hang" problem that would occur in very low entropy sequences.

Skipping regions with high coverage

For a long time, one of the most difficult aspects of using freebayes is that doesn't have a method to skip regions of high coverage. The alignment processing model greatly expands the memory usage relative to depth, leading to problems in high coverage regions.

In cases where coverage varies dramatically across the reference, such as by many orders of magnitude, this led to a need to calculate a coverage map and use this to establish a set of targets. Another approach is to break up the genome into regions of a given number of reads, which tends to normalize runtime across parallel jobs. Both of these approaches are rather complicated for many users to implement, and lead to problems.

This problem is particularly pronounced in the context of assembly polishing, where freebayes is seeing a lot of use. To minimize difficulty for groups using it in this manner (like the VGP), I've implemented a filter that allows us to skip regions of high coverage, --skip-coverage.

I have also renamed the previously used --max-coverage to --limit-coverage to minimize confusion about its function. It applies deterministic read downsampling to drop to the desired coverage. This reduces genotyping cost, but it doesn't help improve runtime in cases of extreme depth because we have to spend a lot of time and memory processing the input alignments. Both options can be applied together, as they are independent.

This release bundles up a number of other changes from the last year.

Attached to this release is an experimental static binary that should work on modern Linux systems. Note that this includes a minor bugfix to correct parameter parsing against v1.3.0.