Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
---|---|---|---|---|---|---|
string_view_needs_cxx17.patch | string_view requires C++-17 | Pierre Gruet <pgt@debian.org> | yes | 2022-07-26 | ||
no_download_of_dependencies.patch | not downloading anything, using the Debian packages | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
using_htslib_from_component.patch | genomicsdb needs a fork of htslib, which is too different from the Debian-packaged one. We provide it as a component. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
using_timedb_from_component.patch | genomicsdb requires a fork of tiledb which is too different from the Debian-packaged one. We provide it as a component. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
strip_tiledb_CMakeLists.patch | stripping the CMakeLists.txt file of the tiledb component from unneeded git commands, and ignoring unpackaged software. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
ignoring_sdk_to_download.patch | removing references to unpackaged SDK in the code | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
use_shared_protobuf_lib.patch | linking to the shared protobuf library, not to the static one | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
missing_links_in_libs.patch | the links to fmt are missing, adding them | Pierre Gruet <pgt@debian.org> | yes | 2022-07-26 | ||
pom.patch | adding missing dependencies in the pom, and also tweaking a bit the protobuf lines so that .proto files are effectively treated | Pierre Gruet <pgt@debian.org> | yes | 2022-07-26 | ||
no_spark_in_Java_build.patch | excluding the spark classes from the build, we won't be able to handle them as we don't have spark in Debian. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
JsonFormat_methods.patch | a few changes to calls to JsonFormat methods have to be changed when building against protobuf-java-format 1.3 instead of 1.2 | Pierre Gruet <pgt@debian.org> | yes | 2022-07-26 | ||
tests_in_all_target.patch | stopping excluding tests from the all target so tha they are built during the Debian build | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
run_tests_in_not_yet_installed_dir.patch | at the test step, the package has not been installed, so we look for the binaries in the source tree | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
build_jni.patch | building the JNI as a shared lib in the CMake process, and loading it from the canonical Debian path from Java code | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
library_names_and_install_paths.patch | installing the main lib in /usr/lib/<triplet> and the component libs in /usr/lib/<triplet>/genomicsdb. Also we install the headers of the private libraries in a subfolder in /usr/include/genomicsdb. |
Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-27 | ||
htslib_define_PATH_MAX.patch | Define PATH_MAX as it is done in cram/open_trace_file.c if not existent. The definition should be removed from this C file since the header file affects all three C files where this definition is used. |
Andreas Tille <tille@debian.org>, | no | debian | ||
htslib_testShebang.patch | Build with -fPIC instead of -fpic It doesn't make a difference on x86, but is required for linking the library on s390x and sparc64. |
Adrian Bunk <bunk@debian.org> | no | |||
htslib_fix_float_precision | ppc64el float handling fix I dug a bit further and it looks like that sam_parse1() is actually generating a different value for the floats in question, so when they are loaded back for the comparison they are already screwed up because strtod() is used in float_to_le() and so also in u32_to_le(), which are inlined and float_to_le() takes a float and not a double as the first argument the use strtof() instead of strtod() in there looks the best, avoiding a truncation from double to float, which might cause precision issues, specially between different archs (like casts) plus optimization. So the following change fixed the issue for me. |
Gustavo Romero <gromero@linux.vnet.ibm.com> | no | |||
spelling.patch | fixing a tiny spelling error | Pierre Gruet <pgt@debian.org> | yes | 2022-07-26 | ||
handling_rpaths.patch | setting RPATH to contain the path to private libraries, it will be emptied afterwards for the libs that don't need it. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
int_type_initialization.patch | initializing with 0 instead of "" in order to avoid error: cast from const char* to mup::int_type {aka int} loses precision | Pierre Gruet <pgt@debian.org> | yes | 2022-09-11 | ||
missing_inclusion_tiledb_constants.patch | including tiledb_constants.h is necessary so that TILEDB_IO_* definitions are found | Pierre Gruet <pgt@debian.org> | yes | 2022-09-11 | ||
using_debian_packaged_catch2.patch | catch2 is Debian-packaged, the embedded copy in the source of genomicsdb-tiledb is too old, things have improved in lattest versions. | Pierre Gruet <pgt@debian.org> | yes | 2022-09-11 |