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/

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

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

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

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

test/loaders/sharq/CMakeLists.txt | 14 7 + 7 - 0 !
tools/loaders/sharq/CMakeLists.txt | 60 25 + 35 - 0 !
2 files changed, 32 insertions(+), 42 deletions(-)

 use debian packaged re2

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

build/env.cmake | 28 15 + 13 - 0 !
ngs/ngs-python/ngs/LibManager.py | 6 3 + 3 - 0 !
2 files changed, 18 insertions(+), 16 deletions(-)

 use soversions

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/align-info/CMakeLists.txt | 1 1 + 0 - 0 !
test/external/fasterq-dump/CMakeLists.txt | 1 1 + 0 - 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 | 11 11 + 0 - 0 !
test/external/sra-info/CMakeLists.txt | 54 53 + 1 - 0 !
test/external/sra-pileup/CMakeLists.txt | 1 1 + 0 - 0 !
test/external/sra-stat/CMakeLists.txt | 3 3 + 0 - 0 !
test/external/srapath/CMakeLists.txt | 1 1 + 0 - 0 !
test/external/vdb-dump/CMakeLists.txt | 2 2 + 0 - 0 !
test/external/vdb-validate/CMakeLists.txt | 2 2 + 0 - 0 !
test/internal/align/CMakeLists.txt | 1 1 + 0 - 0 !
test/internal/vdb-copy/CMakeLists.txt | 4 4 + 0 - 0 !
test/internal/vdb-diff/CMakeLists.txt | 4 4 + 0 - 0 !
test/libs/kfile_stream/CMakeLists.txt | 1 1 + 0 - 0 !
test/loaders/kar/CMakeLists.txt | 1 1 + 0 - 0 !
tools/external/sra-search/test/CMakeLists.txt | 64 63 + 1 - 0 !
tools/internal/dump_ref_fasta/test/CMakeLists.txt | 7 7 + 0 - 0 !
25 files changed, 194 insertions(+), 9 deletions(-)

 label tests "online" to have an easy option to run/ignore them properly

build/env.cmake | 14 7 + 7 - 0 !
tools/loaders/sharq/CMakeLists.txt | 4 2 + 2 - 0 !
2 files changed, 9 insertions(+), 9 deletions(-)

 prefer dynamic libraries

ngs/ngs-sdk/CMakeLists.txt | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 fix linking target

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

tools/loaders/sharq/CMakeLists.txt | 8 4 + 4 - 0 !
1 file changed, 4 insertions(+), 4 deletions(-)

 fulfill baseline requirement

libs/inc/bm/bmsse2.h | 2 1 + 1 - 0 !
libs/inc/bm/bmutil.h | 4 2 + 2 - 0 !
libs/inc/bm/encoding.h | 3 2 + 1 - 0 !
3 files changed, 5 insertions(+), 4 deletions(-)

---

test/loaders/sharq/CMakeLists.txt | 2 1 + 1 - 0 !
test/loaders/sharq/test-regexpr.cpp | 22 11 + 11 - 0 !
tools/loaders/sharq/CMakeLists.txt | 2 1 + 1 - 0 !
tools/loaders/sharq/fastq_defline_matcher.hpp | 190 102 + 88 - 0 !
tools/loaders/sharq/fastq_defline_parser.hpp | 10 5 + 5 - 0 !
tools/loaders/sharq/fastq_parser.hpp | 2 1 + 1 - 0 !
tools/loaders/sharq/fastq_read.hpp | 12 6 + 6 - 0 !
tools/loaders/sharq/regexpr.hpp | 3 2 + 1 - 0 !
8 files changed, 129 insertions(+), 114 deletions(-)

---

ngs/ngs-python/ngs/LibManager.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix python3.12 string syntax
Bug-Debian: https://bugs.debian.org/1087096

ngs/ngs-python/setup.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

---

libs/inc/bm/bm.h | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 [patch] fixed clang compilation issues

tools/external/driver-tool/json-parse.hpp | 2 2 + 0 - 0 !
tools/external/driver-tool/tool-args.hpp | 1 1 + 0 - 0 !
tools/test-tools/qa-stats/input.hpp | 1 1 + 0 - 0 !
tools/test-tools/sam-analyze/alig.hpp | 1 1 + 0 - 0 !
tools/test-tools/sam-factory/sam-factory.cpp | 1 1 + 0 - 0 !
5 files changed, 6 insertions(+)

---

.gitignore | 8 8 + 0 - 0 !
1 file changed, 8 insertions(+)

 update .gitignore from debian packaging branch

The Debian packaging git branch contains these updates to the upstream
.gitignore file(s).  This patch is autogenerated, to provide these
updates to users of the official Debian archive view of the package.

[dgit (12.11) update-gitignore]