[med-svn] [Git][med-team/sra-sdk][master] 18 commits: New upstream version 3.4.1+dfsg
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Mon Sep 28 02:11:26 BST 2026
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
50a25bf2 by Aaron M. Ucko at 2026-08-29T23:56:17-04:00
New upstream version 3.4.1+dfsg
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7a9821e5 by Aaron M. Ucko at 2026-09-06T14:13:12-04:00
Merge tag upstream/3.4.1+dfsg (#1144917).
Under upstream version 3.4.1(+dfsg), test-sra no longer crashes under
glibc 2.43.
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88a61ef3 by Aaron M. Ucko at 2026-09-06T14:17:28-04:00
debian/patches: Update existing patches for new release.
Notably:
* bypass-libxml2-ATTRIBUTE_UNUSED.patch, fix_bm_for_gcc15.patch:
Disable (fully superseded).
* include_cstdint_for_gcc15.patch: Drop superseded portion.
* label_online_tests.patch: Resync; leave out Test_NGS_Python_install.
* link_vdb_dynamically.patch, prefer_dynamic_libraries.patch: Drop
build/env.cmake changes; we can now set DYNAMIC_LINK=ON instead.
* setuptools.patch: Repurpose somewhat. (setup.py has already
migrated to setuptools, but the new accompanying test-install.sh
[Test_NGS_Python_install] uses pip and needs patching to take
infrastructure wheels from the local filesystem rather than PyPI.)
* support_libre2-11.patch, use_debian_packaged_*.patch: Resync.
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4afdbc36 by Aaron M. Ucko at 2026-09-06T14:24:27-04:00
Add debian/patches/public_version-hash.patch.
In tools/loaders/sharq/version.h, #include <kapp/version-hash.h>
without a leading ../libs/, which works only when building against
uninstalled VDB. (As of 3.4.1, Debian's installation makes the header
public.)
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03575e91 by Aaron M. Ucko at 2026-09-06T21:34:01-04:00
Add debian/patches/not_just_ubuntu.patch.
Don't use a build-wide Python virtual env. under Debian (or any other
derivative) either.
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63d9475a by Aaron M. Ucko at 2026-09-06T21:34:42-04:00
debian/rules: Don't clean "expected" (golden) *.orig files.
To that end, move custom cleanup logic to override_dh_clean (vs.
_autoclean).
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e56a4d5e by Aaron M. Ucko at 2026-09-06T21:35:04-04:00
Reflect libkapp.a (partial) takeover from ncbi-vdb.
* debian/control: Bump libngs-c++-dev Breaks/Replaces on libncbi-vdb-dev
to (<< 3.4) per libkapp.a takeover. (NB: sra-sdk took over the name
and the main() wrapper, but ncbi-vdb retained the remaining content
under the name libvdbapp.a.)
* debian/not-installed: Broaden lib*ngs*-static.a to lib*-static.a.
* debian/rules (override_dh_auto_install): Add libkapp.a* to
libngs-c++-dev.
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704bb4b8 by Aaron M. Ucko at 2026-09-06T21:35:12-04:00
debian/rules: Add execute_after_dh_auto_build for javadoc.
Take over javadoc invocation from the upstream build system, which no
longer ever runs javadoc itself.
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11b92915 by Aaron M. Ucko at 2026-09-06T21:35:12-04:00
override_dh_auto_configure: Set the new DYNAMIC_LINK option to ON
... thereby linking dynamically against dependencies in most
cases. (Some portions of the tree still need patching to do so.)
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8cf7fbad by Aaron M. Ucko at 2026-09-06T21:35:12-04:00
debian/control: Adjust build dependencies.
Bump B-D on libncbi-vdb-dev to (>= 3.4.1+dfsg~) and add one on
python3-setuptools-whl to support Test_NGS_Python_install's patch.
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e335e81a by Aaron M. Ucko at 2026-09-06T21:45:14-04:00
Add debian/patches/tiny_csra_shell.patch.
Run test/external/fasterq-dump/tiny_csra.sh under bash per its use of
[[. (As is, it could never officially fail. No further changes
needed, though.)
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26686309 by Aaron M. Ucko at 2026-09-06T22:52:05-04:00
Standards-Version: 4.7.4 (routine-update)
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3d0c3959 by Aaron M. Ucko at 2026-09-06T22:52:16-04:00
Changes made by cme
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03a3ce8c by Aaron M. Ucko at 2026-09-06T22:52:20-04:00
Drop 'Rules-Requires-Root: no' from d/control (routine-update)
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6789359a by Aaron M. Ucko at 2026-09-06T21:52:22-05:00
Reformat the Last-Update date as ISO YYYY-MM-DD.
Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/set_explicit_path_to_schemata.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/skip_test_using_lots_of_memory.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/find_ncbi-vdb-interfaces.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/link_vdb_dynamically.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/use_debian_packaged_re2.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/use_debian_packaged_compression_libs.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/use_soversions.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/label_online_tests.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/prefer_dynamic_libraries.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/fix_ngs-c++-underlinkage.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/use_c_locale_for_comma.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html
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531b38bb by Aaron M. Ucko at 2026-09-27T21:02:30-04:00
debian/copyright: Revisit per licenserecon (lrc).
* Add stanzas for bxzstr, rwqueue, SparkKMer.java, sse2neon.h,
taskflow (complete with internal special cases), and tsl.
* Wildcard (N. Lohmann's) json.hpp.
* Extend BitMagic (libs/inc/bm) date range.
* Formally rename BSD-3-clause-CLI11 to BSD-3-clause, uncontended.
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b41ebd89 by Aaron M. Ucko at 2026-09-27T21:02:30-04:00
d/tests/run-unit-test: Stop testing cache-mgr, retired upstream.
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4b471fa3 by Aaron M. Ucko at 2026-09-27T21:07:57-04:00
Finalize sra-sdk 3.4.1+dfsg-1 for unstable.
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910 changed files:
- CHANGES.md
- README.md
- build/Makefile.env
- build/Makefile.vers
- build/docker/Dockerfile.build-alpine
- + build/docker/Dockerfile.build-alpine-debug
- build/docker/Makefile
- build/env.cmake
- + build/test.cpp
- debian/changelog
- debian/control
- debian/copyright
- debian/not-installed
- debian/patches/find_ncbi-vdb-interfaces.patch
- debian/patches/fix_arm64_build.patch
- debian/patches/fix_ngs-c++-underlinkage.patch
- debian/patches/include_cstdint_for_gcc15.patch
- debian/patches/label_online_tests.patch
- debian/patches/link_vdb_dynamically.patch
- debian/patches/no_sse4.2.patch
- + debian/patches/not_just_ubuntu.patch
- debian/patches/prefer_dynamic_libraries.patch
- + debian/patches/public_version-hash.patch
- debian/patches/series
- debian/patches/set_explicit_path_to_schemata.patch
- debian/patches/setuptools.patch
- debian/patches/skip_test_using_lots_of_memory.patch
- debian/patches/support_libre2-11.patch
- + debian/patches/tiny_csra_shell.patch
- debian/patches/use_c_locale_for_comma.patch
- debian/patches/use_debian_packaged_compression_libs.patch
- debian/patches/use_debian_packaged_re2.patch
- debian/patches/use_soversions.patch
- debian/rules
- debian/tests/run-unit-test
- libs/CMakeLists.txt
- libs/ascp/ascp.c
- libs/ascp/bsd/ascp-path.c
- libs/ascp/linux/ascp-path.c
- libs/ascp/mac/ascp-path.c
- libs/ascp/win/ascp-path.c
- libs/diagnose/diagnose.c
- libs/inc/JSON_ostream.hpp
- − libs/inc/bm/LICENSE
- libs/inc/bm/bm.h
- libs/inc/bm/bmaggregator.h
- libs/inc/bm/bmalgo_impl.h
- libs/inc/bm/bmblocks.h
- libs/inc/bm/bmbmatrix.h
- libs/inc/bm/bmbuffer.h
- libs/inc/bm/bmconst.h
- libs/inc/bm/bmdbg.h
- libs/inc/bm/bmdef.h
- libs/inc/bm/bmfunc.h
- libs/inc/bm/bmserial.h
- libs/inc/bm/bmsparsevec.h
- libs/inc/bm/bmsparsevec_algo.h
- libs/inc/bm/bmsparsevec_compr.h
- libs/inc/bm/bmsparsevec_serial.h
- libs/inc/bm/bmsse4.h
- libs/inc/bm/bmstrsparsevec.h
- libs/inc/bm/bmutil.h
- libs/inc/bm/encoding.h
- libs/inc/fingerprint.hpp
- + libs/inc/flag-stat.hpp
- libs/inc/hashing.hpp
- + libs/inc/kapp/main.h
- libs/inc/kfile_stream/kfile_interface.hpp
- libs/inc/kfile_stream/kfile_stream.hpp
- libs/inc/ngs-vdb/FragmentBlob.hpp
- libs/inc/ngs-vdb/FragmentBlobIterator.hpp
- libs/inc/ngs-vdb/ReferenceBlob.hpp
- libs/inc/ngs-vdb/ReferenceBlobIterator.hpp
- + libs/inc/update-bm.sh
- libs/inc/vdb.hpp
- + libs/kapp/CMakeLists.txt
- + libs/kapp/Makefile
- + libs/kapp/main-priv.h
- + libs/kapp/main.c
- + libs/kapp/unix/sysmain.c
- + libs/kapp/win/sysmain.c
- libs/kxml/xml.c
- libs/loader/loader-meta.c
- libs/ngs-vdb/FragmentBlob.cpp
- libs/ngs-vdb/ReferenceBlobIterator.cpp
- libs/ngs-vdb/VdbReadCollection.cpp
- libs/ngs-vdb/test/CMakeLists.txt
- libs/ngs-vdb/test/CSRA1PileupTest.cpp
- libs/ngs-vdb/test/CSRA1test.cpp
- libs/ngs-vdb/test/SRADBtest.cpp
- libs/ngs-vdb/test/SRAtest.cpp
- libs/ngs-vdb/test/ngsfixture.hpp
- libs/ngs-vdb/test/ngstest.cpp
- libs/ngs-vdb/test/ngstest_byteblob.cpp
- libs/ngs-vdb/test/ngstest_csra1.cpp
- libs/ngs-vdb/test/ngstest_csra1_pileup.cpp
- libs/ngs-vdb/test/ngstest_csra1_readcollection.cpp
- libs/ngs-vdb/test/ngstest_csra1_refwin.cpp
- libs/ngs-vdb/test/ngstest_fragmentblob.cpp
- libs/ngs-vdb/test/ngstest_makedb.cpp
- libs/ngs-vdb/test/ngstest_reference.cpp
- libs/ngs-vdb/test/ngstest_referenceblob.cpp
- libs/ngs-vdb/test/ngstest_sra.cpp
- libs/ngs-vdb/test/ngstest_sradb.cpp
- libs/ngs-vdb/test/test-ngs-vdb.cpp
- libs/schema/insdc/sra.vschema
- libs/vdb-sqlite/CMakeLists.txt
- ngs/CHANGES.md
- ngs/ncbi/ngs/CSRA1_Pileup.c
- ngs/ncbi/ngs/CSRA1_PileupEvent.c
- ngs/ncbi/ngs/NGS_ReadCollection.c
- ngs/ngs-bam/Makefile.vers
- ngs/ngs-java/CMakeLists.txt
- ngs/ngs-java/Makefile.vers
- ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java
- ngs/ngs-python/.gitignore
- ngs/ngs-python/CMakeLists.txt
- ngs/ngs-python/Makefile.vers
- ngs/ngs-python/examples/CMakeLists.txt
- ngs/ngs-python/setup.py
- + ngs/ngs-python/test-install.sh
- ngs/ngs-sdk/Makefile.vers
- ngs/ngs-sdk/dispatch/version.h
- ngs/ngs-sdk/examples/PileupTest.cpp
- + scripts/sra_fingerprint_module.py
- + scripts/sra_fingerprint_test.py
- scripts/test-volume-mgr.pl
- setup/install.prl
- shared/toolkit.vers
- shared/toolkit.vers.h
- test/CMakeLists.txt
- test/external/driver-tool/CMakeLists.txt
- test/external/driver-tool/test-accession.cpp
- test/external/driver-tool/test-build-version.cpp
- test/external/driver-tool/test-command-line.cpp
- test/external/driver-tool/test-filepath.cpp
- test/external/driver-tool/test-json-parse.cpp
- test/external/driver-tool/test-run-source.cpp
- test/external/driver-tool/test-sdl-response.cpp
- test/external/driver-tool/test-sratools.cpp
- test/external/driver-tool/test-tool-args.cpp
- test/external/driver-tool/test-uuid.cpp
- test/external/fasterq-dump/CMakeLists.txt
- + test/external/fasterq-dump/full_test/SOURCES/csra.ini
- + test/external/fasterq-dump/full_test/SOURCES/csra_1rd.ini
- + test/external/fasterq-dump/full_test/SOURCES/csra_400k.ini
- + test/external/fasterq-dump/full_test/SOURCES/csra_bad_qual.ini
- + test/external/fasterq-dump/full_test/SOURCES/csra_bad_rd_len.ini
- + test/external/fasterq-dump/full_test/SOURCES/csra_bad_rd_start.ini
- + test/external/fasterq-dump/full_test/SOURCES/csra_bad_read.ini
- + test/external/fasterq-dump/full_test/SOURCES/csra_cmp.ini
- + test/external/fasterq-dump/full_test/SOURCES/csra_large.ini
- + test/external/fasterq-dump/full_test/SOURCES/db_bad_qual.ini
- + test/external/fasterq-dump/full_test/SOURCES/db_bad_rd_len.ini
- + test/external/fasterq-dump/full_test/SOURCES/db_bad_rd_start.ini
- + test/external/fasterq-dump/full_test/SOURCES/db_bad_read.ini
- + test/external/fasterq-dump/full_test/SOURCES/db_large_reads.ini
- + test/external/fasterq-dump/full_test/SOURCES/db_with_name.ini
- + test/external/fasterq-dump/full_test/SOURCES/db_without_name.ini
- + test/external/fasterq-dump/full_test/SOURCES/flat_bad_qual.ini
- + test/external/fasterq-dump/full_test/SOURCES/flat_bad_rd_len.ini
- + test/external/fasterq-dump/full_test/SOURCES/flat_bad_rd_start.ini
- + test/external/fasterq-dump/full_test/SOURCES/flat_bad_read.ini
- + test/external/fasterq-dump/full_test/SOURCES/flat_large_reads.ini
- + test/external/fasterq-dump/full_test/SOURCES/flat_with_name.ini
- + test/external/fasterq-dump/full_test/SOURCES/flat_without_name.ini
- + test/external/fasterq-dump/full_test/TESTS/CONCAT_NOTECH_FILE.ini
- + test/external/fasterq-dump/full_test/TESTS/CONCAT_NOTECH_STDOUT.ini
- + test/external/fasterq-dump/full_test/TESTS/CONCAT_WTECH_FILE.ini
- + test/external/fasterq-dump/full_test/TESTS/CONCAT_WTECH_STDOUT.ini
- + test/external/fasterq-dump/full_test/TESTS/FASTA_UNSORTED.ini
- + test/external/fasterq-dump/full_test/TESTS/FASTA_US_NOTECH.ini
- + test/external/fasterq-dump/full_test/TESTS/FASTA_US_WTECH.ini
- + test/external/fasterq-dump/full_test/TESTS/SPLIT3_NOTECH.ini
- + test/external/fasterq-dump/full_test/TESTS/SPLIT3_WTECH.ini
- + test/external/fasterq-dump/full_test/TESTS/SPLIT_NOTECH.ini
- + test/external/fasterq-dump/full_test/TESTS/SPLIT_WTECH.ini
- + test/external/fasterq-dump/full_test/TESTS/SPOT_NOTECH_FILE.ini
- + test/external/fasterq-dump/full_test/TESTS/SPOT_NOTECH_STDOUT.ini
- + test/external/fasterq-dump/full_test/TESTS/SPOT_WTECH_FILE.ini
- + test/external/fasterq-dump/full_test/TESTS/SPOT_WTECH_STDOUT.ini
- + test/external/fasterq-dump/full_test/invalid.ini
- + test/external/fasterq-dump/full_test/root.ini
- + test/external/fasterq-dump/full_test/run.sh
- + test/external/fasterq-dump/full_test/test_acc.ini
- + test/external/fasterq-dump/full_test/test_suite.ini
- + test/external/fasterq-dump/full_test/unsorted.ini
- + test/external/fasterq-dump/longreads.sh
- + test/external/fasterq-dump/no_seq_tbl_meta.sh
- test/external/kdbmeta/CMakeLists.txt
- test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ALTREAD/idx0 → test/external/kdbmeta/expected/A
- + test/external/kdbmeta/expected/A_B
- + test/external/kdbmeta/expected/B
- + test/external/kdbmeta/expected/col
- + test/external/kdbmeta/expected/col.AB
- + test/external/kdbmeta/expected/col.schema
- + test/external/kdbmeta/expected/db
- + test/external/kdbmeta/expected/db.AB
- + test/external/kdbmeta/expected/db.SOFTWARE
- + test/external/kdbmeta/expected/db.schema
- + test/external/kdbmeta/expected/tbl
- + test/external/kdbmeta/expected/tbl.AB
- + test/external/kdbmeta/expected/tbl.STATS
- + test/external/kdbmeta/expected/tbl.col
- + test/external/kdbmeta/expected/tbl.schema
- + test/external/kdbmeta/test-meta-delete.sh
- + test/external/kdbmeta/test-update-expr.sh
- + test/external/kdbmeta/test-update-file.sh
- + test/external/kdbmeta/test.sra
- test/external/ngs-pileup/runtestcase.sh
- test/external/ngs-pileup/test-ngs-pileup.cpp
- test/external/ngs/ngs-python/CMakeLists.txt
- + test/external/ngs/ngs-python/test-python.sh
- test/external/ngs/testy-the-bear/CMakeLists.txt
- test/external/ngs/testy-the-bear/testy-the-bear.cpp
- test/external/prefetch/CMakeLists.txt
- test/external/prefetch/out_dir_and_file.pl
- test/external/prefetch/runtests.sh
- test/external/prefetch/test-bad-kart.sh
- + test/external/prefetch/test-caching-disabled.sh
- + test/external/prefetch/test-out-file.sh
- test/external/prefetch/test-quality.cpp
- test/external/sam-dump/Makefile
- test/external/sam-dump/sam_to_csra.sh
- test/external/sra-info/CMakeLists.txt
- + test/external/sra-info/expected/13.0.stdout
- + test/external/sra-info/expected/13.1.stdout
- + test/external/sra-info/expected/13.2.stdout
- + test/external/sra-info/expected/13.3.stdout
- + test/external/sra-info/expected/13.4.stdout
- + test/external/sra-info/expected/14.0.stdout
- + test/external/sra-info/expected/14.1.stdout
- + test/external/sra-info/expected/14.2.stdout
- + test/external/sra-info/expected/14.3.stdout
- + test/external/sra-info/expected/15.0.stdout
- + test/external/sra-info/expected/15.1.stdout
- + test/external/sra-info/expected/15.2.stdout
- + test/external/sra-info/expected/15.3.stdout
- + test/external/sra-info/expected/16.0.stdout
- + test/external/sra-info/expected/16.1.stdout
- + test/external/sra-info/expected/16.2.stdout
- + test/external/sra-info/expected/16.3.stdout
- test/external/sra-info/expected/2.0.stdout
- test/external/vdb-dump/input/platforms/tbl/SEQUENCE/md/cur → test/external/sra-info/input/Test_Sra_Info_Fingerprint/md/cur
- + test/external/sra-info/input/Test_Sra_Info_Fingerprint/md5
- test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ORIGINAL_QUALITY/idx0 → test/external/sra-info/input/Test_Sra_Info_Fingerprint/tbl/SEQUENCE/col/.gitignore
- + test/external/sra-info/input/Test_Sra_Info_Fingerprint/tbl/SEQUENCE/idx/skey
- + test/external/sra-info/input/Test_Sra_Info_Fingerprint/tbl/SEQUENCE/idx/skey.md5
- + test/external/sra-info/input/Test_Sra_Info_Fingerprint/tbl/SEQUENCE/md/cur
- + test/external/sra-info/input/Test_Sra_Info_Fingerprint/tbl/SEQUENCE/md5
- test/external/vdb-dump/input/platforms/md/cur → test/external/sra-info/input/Test_Sra_Info_Fingerprint_None.sra
- test/external/sra-info/test-sra-info.cpp
- test/external/sra-stat/CMakeLists.txt
- test/external/sra-stat/testAssemblyStatistics.cpp
- test/external/vdb-config/CMakeLists.txt
- test/external/vdb-config/model.sh
- test/external/vdb-config/test-vdb-config-model.cpp
- test/external/vdb-dump/CMakeLists.txt
- test/external/vdb-dump/expected/7.0.stdout
- + test/external/vdb-dump/input/README.md
- + test/external/vdb-dump/input/platforms
- − test/external/vdb-dump/input/platforms/md5
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ALTREAD/data
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ALTREAD/idx
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ALTREAD/idx1
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ALTREAD/idx2
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ALTREAD/md/cur
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ALTREAD/md5
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ORIGINAL_QUALITY/data
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ORIGINAL_QUALITY/idx
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ORIGINAL_QUALITY/idx1
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ORIGINAL_QUALITY/idx2
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ORIGINAL_QUALITY/md/cur
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/ORIGINAL_QUALITY/md5
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/PLATFORM/data
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/PLATFORM/idx
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/PLATFORM/idx0
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/PLATFORM/idx1
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/PLATFORM/idx2
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/PLATFORM/md/cur
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/PLATFORM/md5
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/RAW_NAME/data
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/RAW_NAME/idx
- − test/external/vdb-dump/input/platforms/tbl/SEQUENCE/col/RAW_NAME/idx0
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- + test/test-tools/qa-stats/expected/Test_qa_stats_7.1.fastq.stdout
- + test/test-tools/qa-stats/expected/Test_qa_stats_7.2.fastq.stdout
- + test/test-tools/qa-stats/expected/Test_qa_stats_7.3.fastq.stdout
- + test/test-tools/qa-stats/expected/Test_qa_stats_8.0.fastq.stdout
- + test/test-tools/qa-stats/expected/Test_qa_stats_8.1.fastq.stdout
- + test/test-tools/qa-stats/expected/Test_qa_stats_9.0.fastq.stdout
- + test/test-tools/qa-stats/expected/Test_qa_stats_ERR3487613.fasta.stdout
- test/test-tools/qa-stats/expected/Test_qa_stats_Finger_1.stdout
- test/test-tools/qa-stats/expected/Test_qa_stats_Finger_2.stdout
- + test/test-tools/qa-stats/expected/Test_qa_stats_unaligned.fastq.stdout
- + test/test-tools/qa-stats/input/1000.err.sam
- − test/test-tools/qa-stats/input/12.1.fastq
- − test/test-tools/qa-stats/input/14.0.fasta
- − test/test-tools/qa-stats/input/18.0.fastq
- − test/test-tools/qa-stats/input/3.3a.fastq
- − test/test-tools/qa-stats/input/3.3b.fastq
- − test/test-tools/qa-stats/input/3.4b.fastq
- − test/test-tools/qa-stats/input/4.8.fastq
- − test/test-tools/qa-stats/input/4.fastq
- + test/test-tools/qa-stats/runtest-flagstat.sh
- test/test-tools/qa-stats/runtestcase.sh
- test/test-tools/qa-stats/runtests.sh
- test/test-tools/qa-stats/test-finger.cpp
- test/test-tools/qa-stats/test-input.cpp
- test/test-tools/qa-stats/test-output.cpp
- test/vdb/test-vdb.cpp
- test/vdb/test-wvdb.cpp
- tools/CMakeLists.txt
- tools/external/CMakeLists.txt
- tools/external/align-info/CMakeLists.txt
- tools/external/align-info/align-info.c
- − tools/external/cache-mgr/cache-mgr.c
- tools/external/driver-tool/CMakeLists.txt
- tools/external/driver-tool/README.md
- tools/external/driver-tool/common-arguments.h
- tools/external/driver-tool/generate-args-info.sh
- tools/external/driver-tool/json-parse.hpp
- tools/external/driver-tool/sratools.cpp
- tools/external/driver-tool/tool-args.cpp
- tools/external/driver-tool/tool-args.hpp
- tools/external/driver-tool/tool-arguments.h
- tools/external/fasterq-dump/CMakeLists.txt
- tools/external/fasterq-dump/align_iter.c
- tools/external/fasterq-dump/arg_helper.c
- tools/external/fasterq-dump/cleanup_task.c
- tools/external/fasterq-dump/cleanup_task.h
- tools/external/fasterq-dump/cmn_iter.c
- tools/external/fasterq-dump/cmn_iter.h
- tools/external/fasterq-dump/copy_machine.c
- tools/external/fasterq-dump/db_join.c
- tools/external/fasterq-dump/fasterq-dump.c
- tools/external/fasterq-dump/flex_printer.c
- tools/external/fasterq-dump/fq_seq_csra_iter.c
- tools/external/fasterq-dump/fq_seq_csra_iter.h
- tools/external/fasterq-dump/fq_seq_ua_iter.c
- tools/external/fasterq-dump/fq_seq_ua_iter.h
- tools/external/fasterq-dump/helper.c
- tools/external/fasterq-dump/helper.h
- + tools/external/fasterq-dump/idx_to_name.c
- + tools/external/fasterq-dump/idx_to_name.h
- tools/external/fasterq-dump/index.c
- tools/external/fasterq-dump/inspector.c
- tools/external/fasterq-dump/inspector.h
- tools/external/fasterq-dump/lookup_reader.c
- tools/external/fasterq-dump/lookup_writer.c
- tools/external/fasterq-dump/lookup_writer.h
- tools/external/fasterq-dump/merge_sorter.c
- tools/external/fasterq-dump/merge_sorter.h
- tools/external/fasterq-dump/multi_writer.c
- tools/external/fasterq-dump/progress_thread.c
- tools/external/fasterq-dump/raw_read_iter.c
- tools/external/fasterq-dump/ref_inventory.c
- tools/external/fasterq-dump/sbuffer.c
- tools/external/fasterq-dump/sbuffer.h
- tools/external/fasterq-dump/sorter.c
- tools/external/fasterq-dump/sorter.h
- tools/external/fasterq-dump/tbl_join.c
- tools/external/fasterq-dump/tbl_join.h
- tools/external/fasterq-dump/temp_registry.c
- tools/external/fasterq-dump/temp_registry.h
- − tools/external/fasterq-dump/todo.txt
- tools/external/fasterq-dump/tool_ctx.c
- tools/external/fasterq-dump/tool_ctx.h
- tools/external/kdbmeta/CMakeLists.txt
- tools/external/kdbmeta/kdbmeta.c
- tools/external/ngs-pileup/CMakeLists.txt
- tools/external/ngs-pileup/main.cpp
- tools/external/prefetch/CMakeLists.txt
- tools/external/prefetch/PrfMain.c
- tools/external/prefetch/PrfMain.h
- tools/external/prefetch/PrfOutFile.c
- tools/external/prefetch/prefetch.c
- tools/external/rcexplain/CMakeLists.txt
- tools/external/rcexplain/rcexplain.c
- tools/external/ref-variation/ref-variation.cpp
- tools/external/ref-variation/var-expand.cpp
- tools/external/sra-dump/CMakeLists.txt
- tools/external/sra-dump/core.c
- tools/external/sra-dump/fastq.c
- tools/external/sra-dump/illumina.c
- tools/external/sra-dump/sra-dump.c
- tools/external/sra-info/CMakeLists.txt
- tools/external/sra-info/formatter.cpp
- tools/external/sra-info/formatter.hpp
- tools/external/sra-info/main.cpp
- tools/external/sra-info/sra-info.cpp
- tools/external/sra-info/sra-info.hpp
- tools/external/sra-pileup/CMakeLists.txt
- tools/external/sra-pileup/sam-dump.c
- tools/external/sra-pileup/sam-dump3.c
- tools/external/sra-pileup/sra-pileup.c
- tools/external/sra-search/CMakeLists.txt
- tools/external/sra-search/main.cpp
- tools/external/sra-search/searchblock.cpp
- tools/external/sra-search/test/CMakeLists.txt
- tools/external/sra-search/test/test-searchblock.cpp
- tools/external/sra-search/test/test-sra-search-slow.cpp
- tools/external/sra-search/test/test-sra-search.cpp
- tools/external/sra-search/vdb-search.cpp
- tools/external/sra-stat/CMakeLists.txt
- tools/external/sra-stat/sra-stat.c
- tools/external/srapath/CMakeLists.txt
- tools/external/srapath/cgi_request.c
- tools/external/srapath/srapath.c
- tools/external/test-sra/CMakeLists.txt
- tools/external/test-sra/test-sra.c
- tools/external/vdb-config/CMakeLists.txt
- tools/external/vdb-config/configure.cpp
- tools/external/vdb-config/util.cpp
- tools/external/vdb-config/util.hpp
- tools/external/vdb-config/vdb-config.c
- tools/external/vdb-decrypt/CMakeLists.txt
- tools/external/vdb-decrypt/shared.h
- tools/external/vdb-decrypt/vdb-decrypt.c
- tools/external/vdb-decrypt/vdb-encrypt.c
- tools/external/vdb-dump/CMakeLists.txt
- tools/external/vdb-dump/vdb-dump.c
- tools/external/vdb-dump/vdb_info.c
- tools/external/vdb-validate/CMakeLists.txt
- tools/external/vdb-validate/check-corrupt.cpp
- tools/external/vdb-validate/main.c
- tools/external/vdb-validate/vdb-validate.c
- tools/internal/CMakeLists.txt
- tools/internal/align-cache/CMakeLists.txt
- tools/internal/align-cache/align-cache.cpp
- tools/internal/ccextract/CMakeLists.txt
- tools/internal/ccextract/ccextract.c
- tools/internal/check-redact/CMakeLists.txt
- tools/internal/check-redact/check-redact.c
- tools/internal/compute-coverage/CMakeLists.txt
- − tools/internal/compute-coverage/compute-coverage-ngs.cpp
- tools/internal/compute-coverage/compute-coverage.cpp
- tools/internal/copycat/CMakeLists.txt
- tools/internal/copycat/cccat.c
- tools/internal/copycat/cctree-dump.c
- tools/internal/copycat/copycat.c
- tools/internal/dump_ref_fasta/CMakeLists.txt
- tools/internal/dump_ref_fasta/DumpReferenceFASTA.cpp
- tools/internal/make-read-filter/CMakeLists.txt
- tools/internal/make-read-filter/make-read-filter.c
- tools/internal/md5cp/CMakeLists.txt
- tools/internal/md5cp/md5cp.c
- tools/internal/meta-cmp/CMakeLists.txt
- tools/internal/meta-cmp/meta-cmp.c
- tools/internal/meta-copy/CMakeLists.txt
- tools/internal/meta-copy/meta-copy.c
- tools/internal/meta-repair/CMakeLists.txt
- tools/internal/meta-repair/meta-repair.c
- − tools/internal/rd-filter-redact/rd-filter-redact.c
- − tools/internal/rd-filter-redact/test-read-write-cursor.c
- + tools/internal/read-filter-redact/CMakeLists.txt
- + tools/internal/read-filter-redact/Makefile
- tools/internal/rd-filter-redact/read-filter-redact.c → tools/internal/read-filter-redact/read-filter-redact.cpp
- + tools/internal/shared/teefile.c
- + tools/internal/shared/teefile.h
- + tools/internal/sra-add-fp/CMakeLists.txt
- tools/internal/rd-filter-redact/Makefile → tools/internal/sra-add-fp/Makefile
- + tools/internal/sra-add-fp/main.cpp
- + tools/internal/sra-add-fp/sra-add-fp.sh
- tools/internal/vdb-copy/CMakeLists.txt
- tools/internal/vdb-copy/vdb-copy.c
- tools/internal/vdb-diff/CMakeLists.txt
- tools/internal/vdb-diff/vdb-diff.c
- tools/internal/vdb-sql/CMakeLists.txt
- tools/internal/vdb-sql/fastconv.c
- tools/internal/vdb-sql/vdb_shell.c
- tools/loaders/bam-loader/CMakeLists.txt
- tools/loaders/bam-loader/KVPFile.c
- tools/loaders/bam-loader/bam-loader.c
- tools/loaders/bam-loader/loader-imp.c
- tools/loaders/bam-loader/sam-header-platform.c
- tools/loaders/bam-loader/samview.c
- tools/loaders/cg-load/CMakeLists.txt
- tools/loaders/cg-load/cg-load.c
- tools/loaders/fastq-loader/CMakeLists.txt
- tools/loaders/fastq-loader/common-writer.c
- tools/loaders/fastq-loader/fastq-loader.c
- tools/loaders/general-loader/database-loader.cpp
- tools/loaders/general-loader/main.cpp
- tools/loaders/general-loader/test/test-general-loader.cpp
- tools/loaders/kar/CMakeLists.txt
- tools/loaders/kar/README.txt
- tools/loaders/kar/kar+.c
- tools/loaders/kar/kar+meta.c
- tools/loaders/kar/kar-args.c
- tools/loaders/kar/kar-args.h
- tools/loaders/kar/kar-path.c
- tools/loaders/kar/kar.c
- tools/loaders/kar/sra-kar.c
- tools/loaders/pacbio-load/CMakeLists.txt
- tools/loaders/pacbio-load/pacbio-load.c
- tools/loaders/pacbio-load/pl-context.h
- tools/loaders/sharq/CMakeLists.txt
- + tools/loaders/sharq/CloudFilesystem.cmake
- tools/loaders/sharq/Makefile
- + tools/loaders/sharq/build_sdk/CMakeLists.txt
- + tools/loaders/sharq/build_sdk/InstallCloudSDKs.cmake
- + tools/loaders/sharq/build_sdk/build.sh
- + tools/loaders/sharq/cloud_filesystem.hpp
- tools/loaders/sharq/fastq_defline_matcher.hpp
- tools/loaders/sharq/fastq_defline_parser.hpp
- tools/loaders/sharq/fastq_error.hpp
- tools/loaders/sharq/fastq_parse.cpp
- tools/loaders/sharq/fastq_parser.hpp
- + tools/loaders/sharq/fastq_stream_factory.hpp
- tools/loaders/sharq/fastq_writer.hpp
- + tools/loaders/sharq/istreambuf_holder.hpp
- tools/loaders/sharq/spot_assembly.hpp
- tools/loaders/sharq/version.h
- tools/loaders/sra-load/CMakeLists.txt
- tools/loaders/sra-load/loader.c
- tools/loaders/sra-sort/CMakeLists.txt
- tools/loaders/sra-sort/dump-blob-boundaries.c
- tools/loaders/sra-sort/membank.c
- tools/loaders/sra-sort/run.c
- tools/loaders/sra-sort/sra-sort.c
- tools/loaders/sra-sort/sra-sort.h
- tools/loaders/vdb-lock/CMakeLists.txt
- tools/loaders/vdb-lock/vdb-lock.c
- tools/loaders/vdb-unlock/CMakeLists.txt
- tools/loaders/vdb-unlock/vdb-unlock.c
- tools/test-tools/CMakeLists.txt
- tools/test-tools/crc32sum/CMakeLists.txt
- tools/test-tools/crc32sum/crc32sum.c
- tools/test-tools/kdb-index/CMakeLists.txt
- tools/test-tools/kdb-index/kdb-index.c
- tools/external/cache-mgr/CMakeLists.txt → tools/test-tools/make-platform-test/CMakeLists.txt
- + tools/test-tools/make-platform-test/Makefile
- + tools/test-tools/make-platform-test/make-platform-test.cpp
- tools/test-tools/pacbio-correct/CMakeLists.txt
- tools/test-tools/pacbio-correct/pacbio-correct.c
- tools/test-tools/pileup-stats/CMakeLists.txt
- tools/test-tools/pileup-stats/pileup-stats.cpp
- tools/test-tools/qa-stats/CMakeLists.txt
- tools/test-tools/qa-stats/input.cpp
- tools/test-tools/qa-stats/input.hpp
- tools/test-tools/qa-stats/main.cpp
- tools/test-tools/qa-stats/parameters.hpp
- tools/test-tools/qa-stats/stats.hpp
- tools/test-tools/rnd2sra/CMakeLists.txt
- tools/test-tools/rowwritetest/Makefile → tools/test-tools/rnd2sra/Makefile
- tools/test-tools/rnd2sra/README.txt
- tools/test-tools/rnd2sra/src/bio_or_tech.hpp
- tools/test-tools/rnd2sra/src/csra_seq_cols.hpp
- tools/test-tools/rnd2sra/src/csra_spot.hpp
- tools/test-tools/rnd2sra/src/main_params.hpp
- tools/test-tools/rnd2sra/src/normalizer.hpp
- + tools/test-tools/rnd2sra/src/platform.hpp
- tools/test-tools/rnd2sra/src/rnd2sra.cpp
- tools/test-tools/rnd2sra/src/rnd2sra_ini.hpp
- tools/test-tools/rnd2sra/src/rnd2sra_main.hpp
- tools/test-tools/rnd2sra/src/rnd_cmn.hpp
- tools/test-tools/rnd2sra/src/rnd_csra.hpp
- tools/test-tools/rnd2sra/src/rnd_none_csra.hpp
- tools/test-tools/rnd2sra/src/runner.hpp
- tools/test-tools/rnd2sra/src/runner_ini.hpp
- tools/test-tools/rnd2sra/util/fd_reader.hpp
- tools/test-tools/rnd2sra/util/file_deleter.hpp
- tools/test-tools/rnd2sra/util/file_rename.hpp
- tools/test-tools/rnd2sra/util/file_report.hpp
- tools/test-tools/rnd2sra/util/file_tool.hpp
- + tools/test-tools/rnd2sra/util/fs.hpp
- tools/test-tools/rnd2sra/util/ini.hpp
- tools/test-tools/rnd2sra/util/random_toolbox.hpp
- tools/test-tools/rnd2sra/util/str_tools.hpp
- tools/test-tools/rnd2sra/vdb/VdbObj.hpp
- tools/test-tools/rnd2sra/vdb/kapp.hpp
- − tools/test-tools/rowwritetest/rowwritetest.c
- tools/test-tools/sam-analyze/CMakeLists.txt
- tools/test-tools/sam-analyze/main.cpp
- tools/test-tools/sam-factory/CMakeLists.txt
- tools/test-tools/sam-factory/sam-factory.cpp
- tools/test-tools/samview-util/CMakeLists.txt
- tools/test-tools/samview-util/samview.c
- tools/test-tools/schema-replace/CMakeLists.txt
- tools/test-tools/schema-replace/schema-replace.c
- tools/test-tools/sortreadtest/CMakeLists.txt
- tools/test-tools/sortreadtest/sortreadtest.c
- tools/test-tools/test-download/CMakeLists.txt
- tools/test-tools/test-download/test-download.c
- tools/test-tools/testld/CMakeLists.txt
- tools/test-tools/testld/testld.c
- tools/test-tools/txt2kdb/CMakeLists.txt
- tools/test-tools/txt2kdb/txt2kdb.c
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/c8cab3f5492b0f49c6aeaec36e67072086353ae8...4b471fa37d4fab78e34c851a42d18168a4e7dfd9
--
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/c8cab3f5492b0f49c6aeaec36e67072086353ae8...4b471fa37d4fab78e34c851a42d18168a4e7dfd9
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