| Patch |
File delta |
Description |
| set_explicit_path_to_schemata.patch | (download) |
test/loaders/fastq-loader/test-fastq-loader.cpp |
2 1 + 1 - 0 !
tools/internal/vdb-copy/vdb-copy.kfg |
8 4 + 4 - 0 !
tools/loaders/bam-loader/bam-loader.c |
2 1 + 1 - 0 !
tools/loaders/cg-load/cg-load.c |
2 1 + 1 - 0 !
tools/loaders/fastq-loader/fastq-loader.c |
2 1 + 1 - 0 !
tools/loaders/pacbio-load/pl-context.h |
2 1 + 1 - 0 !
tools/loaders/sra-sort/run.c |
2 1 + 1 - 0 !
tools/test-tools/sortreadtest/sortreadtest.c |
4 2 + 2 - 0 !
8 files changed, 12 insertions(+), 12 deletions(-) |
in debian */*.vschema is installed to /usr/lib/ncbi-vdb/
|
| python3 | (download) |
test/external/sra-pileup/check_skiplist.py |
2 1 + 1 - 0 !
test/external/sra-pileup/test_all_sam_dump_has_spotgroup.py |
2 1 + 1 - 0 !
test/external/sra-pileup/test_diff_fastq_dump_vs_sam_dump.py |
2 1 + 1 - 0 !
test/samline/bx_tag_test.py |
4 2 + 2 - 0 !
test/samline/ca_test.py |
2 1 + 1 - 0 !
test/tarballs/test-tarballs.sh |
2 1 + 1 - 0 !
tools/external/fasterq-dump/fastq-diff.py |
5 2 + 3 - 0 !
7 files changed, 9 insertions(+), 10 deletions(-) |
upgrade from python2 to python 3
|
| skip_test_using_lots_of_memory.patch | (download) |
test/loaders/fastq-loader/test-id2name.cpp |
2 2 + 0 - 0 !
1 file changed, 2 insertions(+) |
skip test that test needs a *lot* of memory -- at
least 4G, quite possibly 8G if there's copying involved
see https://lists.debian.org/debian-med/2021/10/msg00069.html
|
| find_ncbi vdb interfaces.patch | (download) |
CMakeLists.txt |
4 2 + 2 - 0 !
tools/loaders/bam-loader/CMakeLists.txt |
2 1 + 1 - 0 !
tools2/shared/cmake/Findncbi-vdb.cmake |
3 2 + 1 - 0 !
3 files changed, 5 insertions(+), 4 deletions(-) |
find ncbi vdb at debian location
|
| link_vdb_dynamically.patch | (download) |
build/env.cmake |
8 4 + 4 - 0 !
tools/loaders/general-loader/test/CMakeLists.txt |
2 1 + 1 - 0 !
2 files changed, 5 insertions(+), 5 deletions(-) |
link vdb dynamically
|
| use_debian_packaged_re2.patch | (download) |
test/loaders/sharq/CMakeLists.txt |
14 7 + 7 - 0 !
tools/loaders/sharq/CMakeLists.txt |
40 20 + 20 - 0 !
2 files changed, 27 insertions(+), 27 deletions(-) |
use debian packaged re2
|
| use_debian_packaged_compression_libs.patch | (download) |
tools/loaders/bam-loader/CMakeLists.txt |
4 2 + 2 - 0 !
tools/loaders/sra-sort/CMakeLists.txt |
4 2 + 2 - 0 !
2 files changed, 4 insertions(+), 4 deletions(-) |
use debian packaged compression libs
|
| fix_javadoc_build.patch | (download) |
ngs/ngs-java/CMakeLists.txt |
8 4 + 4 - 0 !
1 file changed, 4 insertions(+), 4 deletions(-) |
make sure javadoc builds properly
|
| use_soversions.patch | (download) |
build/env.cmake |
28 15 + 13 - 0 !
ngs/ngs-python/ngs/LibManager.py |
4 2 + 2 - 0 !
2 files changed, 17 insertions(+), 15 deletions(-) |
use soversions
|
| label_online_tests.patch | (download) |
libs/ngs-vdb/test/CMakeLists.txt |
23 19 + 4 - 0 !
ngs/ngs-java/examples/CMakeLists.txt |
2 2 + 0 - 0 !
ngs/ngs-python/examples/CMakeLists.txt |
1 1 + 0 - 0 !
ngs/ngs-sdk/examples/CMakeLists.txt |
2 1 + 1 - 0 !
test/external/kdbmeta/CMakeLists.txt |
1 1 + 0 - 0 !
test/external/ngs-pileup/CMakeLists.txt |
12 11 + 1 - 0 !
test/external/ngs/ngs-java/CMakeLists.txt |
1 1 + 0 - 0 !
test/external/ngs/ngs-python/CMakeLists.txt |
1 1 + 0 - 0 !
test/external/ngs/testy-the-bear/CMakeLists.txt |
2 1 + 1 - 0 !
test/external/prefetch/CMakeLists.txt |
10 10 + 0 - 0 !
test/external/sra-pileup/CMakeLists.txt |
1 1 + 0 - 0 !
test/external/sra-stat/CMakeLists.txt |
2 2 + 0 - 0 !
test/external/srapath/CMakeLists.txt |
1 1 + 0 - 0 !
test/external/vdb-dump/CMakeLists.txt |
1 1 + 0 - 0 !
test/internal/align/CMakeLists.txt |
1 1 + 0 - 0 !
test/internal/vdb-diff/CMakeLists.txt |
4 4 + 0 - 0 !
test/loaders/kar/CMakeLists.txt |
1 1 + 0 - 0 !
tools/external/sra-search/test/CMakeLists.txt |
2 2 + 0 - 0 !
18 files changed, 61 insertions(+), 7 deletions(-) |
label tests "online" to have an easy option to run/ignore them properly
|
| prefer_dynamic_libraries.patch | (download) |
build/env.cmake |
6 3 + 3 - 0 !
tools/loaders/sharq/CMakeLists.txt |
4 2 + 2 - 0 !
2 files changed, 5 insertions(+), 5 deletions(-) |
prefer dynamic libraries
|
| fix_ngs c++ underlinkage.patch | (download) |
ngs/ngs-sdk/CMakeLists.txt |
1 1 + 0 - 0 !
1 file changed, 1 insertion(+) |
fix linking target
|
| use_c_locale_for_comma.patch | (download) |
tools/loaders/bam-loader/loader-imp.c |
2 1 + 1 - 0 !
tools/loaders/sharq/fastq_parse.cpp |
2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-) |
use c locale for comma
|
| no_sse4.2.patch | (download) |
test/loaders/sharq/CMakeLists.txt |
2 1 + 1 - 0 !
tools/loaders/bam-loader/CMakeLists.txt |
6 3 + 3 - 0 !
tools/loaders/sharq/CMakeLists.txt |
8 4 + 4 - 0 !
3 files changed, 8 insertions(+), 8 deletions(-) |
fulfill baseline requirement
|
