Freebayes 1.3.8 does not build

[feghalya]

Building Freebayes v1.3.8 from source seems impossible as it is.

Using meson build -Dprefer_system_deps=false fails because it expects a vcflib submodule, and meson build -Dprefer_system_deps=true fails as well because the fastahack and smithwaterman libraries are hard-coded to use submodules.

The only way meson build worked was cloning vcflib in contrib/ and running meson build -Dprefer_system_deps=false, but then meson test -C build/ would fail because it could not find IntervalTree.h. To solve this, I had to change IntervalTree.h back to ../intervaltree/IntervalTree.h in src/BedReader.h and src/BedReader.cpp.

[twrightsman]

This also currently affects the Debian packaging (https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1067271). See a failed build log here.

[h836472]

Managed to build Freebayes from source with these steps (git repository accessed: 16th December 2024)
1., git clone https://github.com/freebayes/freebayes.git
2., cd freebayes
3., manually edit .gitmodules, correct broken URL for "multichoose" [email protected]:vcflib/multichoose.git to https://github.com/vcflib/multichoose.git
4., git submodule sync
5., git submodule update --init --recursive
6., git submodule add https://github.com/ekg/split.git contrib/split
#all submodule download issue solved there including the addition of forgotten "split" module
7., meson build --buildtype=release
8., cd build
#upon the first ninja attempt, several header files from contrib folder tree were not found. Decided to simply copy them to src
9., cp ../contrib/fastahack/split.h ../src/
10., cp ../contrib/smithwaterman/convert.h ../src/
11., cp ../contrib/split/join.h ../src/
12., cp ../contrib/fastahack/Fasta.h ../src/
13., cp ../contrib/fastahack/Region.h ../src/
14., cp ../contrib/multichoose/multichoose.h ../src/
15., cp ../contrib/multichoose/multipermute.h ../src/
16., ninja