| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| gcc-10 | [PATCH] Make sure std::runtime_error is available This should fix #3170, unless there are more problems on very new GCC. |
Adam Novak <anovak@soe.ucsc.edu> | no | 2021-01-26 | ||
| use_packaged_libdeflate | Use the Debian package for libdeflate | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_jemalloc | Use the Debian packaged version of jemalloc | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_libbackward-cpp | Use the Debian version of cpp-backward | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_elfutils | Use the Debian packages for elfutils | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_raptor2 | Use the Debian package for raptor/rapper | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| no_need_for_snappy | Due to other patches, snappy is no longer a dependency | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_sparsehash | Use the Debian package for sparsehash | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_ssw | Use the Debian packaged version of libssw | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_rapidjson | Since the Debian package of vowpal_wabbit is broken and not in testing/stable; make the local copy use the Debian package of rapidjson | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_fermi-lite | Use the Debian package of fermi-lite Adjust for the renamed bseq1_t→fml_seq1_t See https://github.com/lh3/fermi-lite/issues/5 |
Michael R. Crusoe | not-needed | |||
| spelling | fix spelling typos | Michael R. Crusoe <crusoe@debian.org> | yes | |||
| no_rpath | don't use rpath | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| no_pg | Ensure that we don't accidentally include profile mode | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_fastahack | Use the Debian version of fastahack; not working due to vg needing modifications to the upstream sourcecode | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| hardening_flags | Make build system more flexiblehttps://github.com/benedictpaten/sonLib/pull/42 https://github.com/vgteam/gfakluge/pull/6 https://github.com/yoheirosen/sublinear-Li-Stephens/pull/7 https://github.com/vgteam/vg/pull/3168 https://github.com/vgteam/cpp_progress_bar/pull/2 So that Debian can pass hardening flags |
Michael R. Crusoe <crusoe@debian.org> | yes | |||
| use_packaged_smithwaterman | make the vcflib codecopy less bad by using the smithwaterman library | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| static | For Debian, don't statically link to cairo, jansson, libstdc++, libgcc | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_lz4 | Use the Debian packaged lz4 library | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| parallize_better | improve build parallelization | Michael R. Crusoe <crusoe@debian.org> | yes | |||
| use_packaged_libtsl-hopscotch-map-dev | Use the tsl-hopscotch-map cmake target | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| libVCFH_unneeded | libVCFH is unneeded | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| better_clean | don't clean a file that is part of the distribution tarball | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_vcflib | Attempt to use the Debian version of vcflib | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| use_packaged_htslib | Use the Debian package of htslib | Michael R. Crusoe <crusoe@debian.org> | not-needed | |||
| simde | Increase portability by using SIMD Everywhere library | Michael R. Crusoe <crusoe@debian.org> | yes | |||
| crossbuild | Enable cross building | Michael R. Crusoe <crusoe@debian.org> | yes | |||
| python3 | convert all Python scripts to Python v3 | Michael R. Crusoe <crusoe@debian.org> | yes | |||
| fix-handlegraph | libvgio: fix include path for libhandlegraph It is odd that this is needed... |
Michael R. Crusoe <crusoe@debian.org> | no |