Debian Patches

Status for vg/1.30.0+ds-1

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

All known versions for source package 'vg'

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