[med-svn] [blasr] branch debian/jessie-backports updated (7fbf228 -> 8ebd59c)
Afif Elghraoui
afif at moszumanska.debian.org
Wed Apr 26 06:10:25 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch debian/jessie-backports
in repository blasr.
from 7fbf228 blasr (0~20151014+git8e668be-1~bpo8+1) jessie-backports; urgency=high
adds 9690aa9 Imported Upstream version 5.2
adds b8aaf16 Merge tag 'upstream/5.2'
adds 3a18309 Find PB libraries in the default LD path
adds 3d5b72b Bump Standards-Version to 3.9.8
adds 763ecfe Use encrypted protocols for VCS
adds 3a12f90 Update email address and copyright year
adds 317d7eb Imported Upstream version 5.3
adds 0fc2023 Merge tag 'upstream/5.3'
adds 0eeb861 Update paths to pbseqlib headers
adds 29cad32 Remove unused lintian overrides
adds 38c3d4f Update debian/TODO
adds 1665b8d Add d/NEWS to explain interface change
adds 04692bd d/rules: Minor clean-ups
adds e4999fe releasing package blasr version 5.3-1
adds c476399 Build with pbbam
adds 269af5a Use pbseqlib metapackage rather than depending on individual libraries
adds 456172a Build with pbbam
adds 153c0f9 build bax2bam and bam2bax
adds a5821cc Merge branch 'topic/more-utils'
adds cf7cb6e releasing package blasr version 5.3-2
adds afe0a9b Imported Upstream version 5.3+0
adds 60139c3 Merge tag 'upstream/5.3+0'
adds 1920d57 Refresh patches
adds c6a674f releasing package blasr version 5.3+0-1
new eb92ed2 Merge tag 'debian/5.3+0-1' into debian/jessie-backports
new 8ebd59c releasing package blasr version 5.3+0-1~bpo8+1
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 9 +
Blasr.cpp | 292 +++---
LICENSE | 34 +
README.INSTALL.md | 24 +-
configure.py | 10 +-
cram.mk | 48 +
ctest/.gitignore | 1 +
ctest/affineAlign.t | 6 +-
ctest/aggressiveIntervalCut.t | 8 +-
ctest/alignScore.t | 2 +-
ctest/bamConcordant.t | 33 +
ctest/bamIn.t | 39 +-
ctest/bamOut.t | 4 +-
ctest/bug25328.t | 2 +-
ctest/bug25741.t | 9 -
ctest/bug25766.t | 4 +-
ctest/ccsH5.t | 4 +-
ctest/cigarAdjecentIndels.t | 22 +
ctest/concordant.t | 44 +-
ctest/dataset.t | 64 ++
ctest/deterministic.t | 47 +
ctest/ecoli.t | 13 +-
ctest/fastMaxInterval.t | 8 +-
ctest/filtercriteria.t | 8 +-
ctest/fofn.t | 4 +-
ctest/hitpolicy.t | 18 +-
ctest/holeNumbers.t | 4 +-
ctest/m0-5.t | 10 +-
ctest/multipart.t | 6 +-
ctest/noSplitSubreads.t | 40 +-
ctest/open_fail.t | 2 +-
ctest/samNM.t | 13 -
ctest/setup.sh | 8 +-
ctest/unaligned.t | 25 +
ctest/useccsallBestN1.t | 9 +-
ctest/useccsallLargeGenome.t | 4 +-
ctest/verbose.t | 2 +-
debian/NEWS | 6 +
debian/TODO | 5 +-
debian/changelog | 37 +
debian/control | 20 +-
debian/copyright | 4 +-
debian/install | 2 +
debian/lintian-overrides | 4 -
debian/patches/cmake-utils.patch | 25 +
debian/patches/disable-gtest.patch | 28 +
debian/patches/series | 2 +
debian/rules | 50 +-
extrautils/BasH5Simulator.cpp | 524 ----------
extrautils/CCSH5ToBam.cpp | 135 ---
extrautils/SimpleShredder.cpp | 2 +-
extrautils/ctest/alchemy.t | 20 -
extrautils/ctest/ccsh5tobam.t | 10 -
extrautils/ctest/printTupleCountTable.t | 2 +-
extrautils/makefile | 12 +-
{include => iblasr}/BlasrAlign.hpp | 39 +-
{include => iblasr}/BlasrAlignImpl.hpp | 157 ++-
iblasr/BlasrHeaders.h | 114 +++
iblasr/BlasrMiscs.hpp | 62 ++
{include => iblasr}/BlasrMiscsImpl.hpp | 100 +-
{include => iblasr}/BlasrUtils.hpp | 57 +-
{include => iblasr}/BlasrUtilsImpl.hpp | 111 +--
{include => iblasr}/MappingBuffers.hpp | 52 +-
{include => iblasr}/MappingIPC.h | 30 +-
{include => iblasr}/MappingParameters.h | 160 ++-
{include => iblasr}/MappingSemaphores.h | 15 +-
{include => iblasr}/ReadAlignments.hpp | 45 +-
{include => iblasr}/RegisterBlasrOptions.h | 415 ++++----
{include => iblasr}/RegisterFilterOptions.h | 41 +-
include/BlasrHeaders.h | 149 ---
include/BlasrMiscs.hpp | 100 --
makefile | 40 +-
rules.mk | 9 +-
sub.mk | 9 +
utils/.gitignore | 2 +
utils/LoadPulses.cpp | 145 ++-
utils/PulseToFasta.cpp | 37 +-
utils/SAWriter.cpp | 358 +++----
utils/SDPMatcher.cpp | 39 +-
utils/SamFilter.cpp | 56 +-
utils/SamToCmpH5.cpp | 29 +-
utils/SamToM4.cpp | 26 +-
utils/ToAfg.cpp | 42 +-
utils/bam2bax/BUILD.txt | 68 ++
utils/bam2bax/CMakeLists.txt | 139 +++
utils/bam2bax/README.md | 11 +
utils/bam2bax/makefile | 52 +
utils/bam2bax/src/Bam2Bax.cpp | 29 +
utils/bam2bax/src/Bam2Bax.h | 13 +
utils/bam2bax/src/Bam2BaxConverter.h | 38 +
utils/bam2bax/src/Bam2BaxConverterImpl.hpp | 57 ++
utils/bam2bax/src/Bam2BaxInternal.h | 78 ++
utils/bam2bax/src/Bam2BaxMain.cpp | 75 ++
utils/bam2bax/src/Bam2PlxMain.cpp | 65 ++
utils/bam2bax/src/CMakeLists.txt | 81 ++
utils/bam2bax/src/Converter.cpp | 130 +++
utils/bam2bax/src/Converter.h | 77 ++
utils/bam2bax/src/MetadataWriter.cpp | 42 +
utils/bam2bax/src/MetadataWriter.h | 38 +
utils/bam2bax/src/OptionParser.cpp | 562 +++++++++++
utils/bam2bax/src/OptionParser.h | 306 ++++++
utils/bam2bax/src/RegionTypeAdapter.h | 129 +++
utils/bam2bax/src/RegionsAdapter.h | 118 +++
utils/bam2bax/src/Settings.cpp | 224 +++++
utils/bam2bax/src/Settings.h | 80 ++
utils/bam2bax/tests/CMakeLists.txt | 94 ++
utils/bam2bax/tests/cram/bam2bax.t | 84 ++
utils/bam2bax/tests/cram/bam2plx.t | 230 +++++
...4852550000001823085912221377_s1_X0.1.scraps.bam | Bin 0 -> 644642 bytes
...52550000001823085912221377_s1_X0.1.subreads.bam | Bin 0 -> 220556 bytes
utils/bam2bax/tests/data/tiny.scraps.sam | 18 +
utils/bam2bax/tests/data/tiny.subreads.sam | 27 +
.../bam2bax/tests/data/tiny_bam2plx.polymerase.sam | 4 +
utils/bam2bax/tests/example/end-to-end.sh | 66 ++
utils/bam2bax/tests/files.cmake | 64 ++
.../tests/resequencing/bam2bax_resequencing.py | 179 ++++
utils/bam2bax/tests/resequencing/one_bax_test.sh | 5 +
utils/bam2bax/tests/resequencing/settings.xml | 201 ++++
utils/bam2bax/tests/resequencing/tiny_test.sh | 5 +
utils/bam2bax/tests/src/TestConstants.h | 195 ++++
utils/bam2bax/tests/src/TestData.h.in | 18 +
utils/bam2bax/tests/src/TestUtils.cpp | 42 +
utils/bam2bax/tests/src/TestUtils.h | 13 +
utils/bam2bax/tests/src/test.cpp | 23 +
utils/bam2bax/tests/src/test_Bam2BaxConverter.cpp | 94 ++
.../bam2bax/tests/src/test_HDFBaseCallsWriter.cpp | 56 ++
utils/bam2bax/tests/src/test_HDFBaxWriter.cpp | 100 ++
utils/bam2bax/tests/src/test_HDFScanDataWriter.cpp | 76 ++
.../bam2bax/tests/src/test_HDFZMWMetricsWriter.cpp | 51 +
utils/bam2bax/tests/src/test_HDFZMWWriter.cpp | 40 +
utils/bax2bam/BUILD.txt | 10 +
utils/bax2bam/CMakeLists.txt | 137 +++
utils/bax2bam/README.md | 62 ++
utils/bax2bam/makefile | 34 +
utils/bax2bam/src/Bax2Bam.cpp | 251 +++++
utils/bax2bam/src/Bax2Bam.h | 13 +
utils/bax2bam/src/CMakeLists.txt | 60 ++
utils/bax2bam/src/CcsConverter.cpp | 117 +++
utils/bax2bam/src/CcsConverter.h | 47 +
utils/bax2bam/src/ConverterBase.h | 1023 ++++++++++++++++++++
utils/bax2bam/src/HqRegionConverter.cpp | 192 ++++
utils/bax2bam/src/HqRegionConverter.h | 26 +
utils/bax2bam/src/IConverter.cpp | 78 ++
utils/bax2bam/src/IConverter.h | 53 +
utils/bax2bam/src/OptionParser.cpp | 562 +++++++++++
utils/bax2bam/src/OptionParser.h | 306 ++++++
utils/bax2bam/src/PolymeraseReadConverter.cpp | 60 ++
utils/bax2bam/src/PolymeraseReadConverter.h | 26 +
utils/bax2bam/src/Settings.cpp | 271 ++++++
utils/bax2bam/src/Settings.h | 91 ++
utils/bax2bam/src/SubreadConverter.cpp | 395 ++++++++
utils/bax2bam/src/SubreadConverter.h | 26 +
utils/bax2bam/src/main.cpp | 131 +++
utils/bax2bam/tests/CMakeLists.txt | 90 ++
utils/bax2bam/tests/bax2bam.t | 7 +
utils/bax2bam/tests/files.cmake | 52 +
utils/bax2bam/tests/src/TestData.h.in | 19 +
utils/bax2bam/tests/src/TestUtils.cpp | 43 +
utils/bax2bam/tests/src/TestUtils.h | 13 +
utils/bax2bam/tests/src/test_ccs.cpp | 219 +++++
utils/bax2bam/tests/src/test_common.cpp | 16 +
utils/bax2bam/tests/src/test_hqregions.cpp | 422 ++++++++
utils/bax2bam/tests/src/test_polymerase.cpp | 238 +++++
utils/bax2bam/tests/src/test_subreads.cpp | 416 ++++++++
.../gtest/.deps/test_fused_gtest_test-gtest-all.Po | 1 +
.../.deps/test_fused_gtest_test-gtest_main.Po | 1 +
.../bax2bam/third-party/gtest-1.7.0/lib/.dirstamp | 0
.../gtest-1.7.0/samples/.deps/.dirstamp | 0
.../gtest-1.7.0/samples/.deps/sample1.Plo | 3 +
.../gtest-1.7.0/samples/.deps/sample10_unittest.Po | 1 +
.../gtest-1.7.0/samples/.deps/sample1_unittest.Po | 1 +
.../gtest-1.7.0/samples/.deps/sample2.Plo | 29 +
.../gtest-1.7.0/samples/.deps/sample4.Plo | 48 +
.../samples/.deps/test_fused_gtest_test-sample1.Po | 1 +
.../test_fused_gtest_test-sample1_unittest.Po | 1 +
.../third-party/gtest-1.7.0/samples/.dirstamp | 0
.../third-party/gtest-1.7.0/src/.deps/.dirstamp | 0
.../gtest-1.7.0/src/.deps/gtest-all.Plo | 617 ++++++++++++
.../gtest-1.7.0/src/.deps/gtest_main.Plo | 460 +++++++++
.../bax2bam/third-party/gtest-1.7.0/src/.dirstamp | 0
.../gtest-1.7.0/test/.deps/gtest_all_test.Po | 1 +
utils/ctest/.gitignore | 1 +
utils/ctest/samFilter.t | 24 +-
utils/makefile | 22 +-
184 files changed, 12673 insertions(+), 2348 deletions(-)
create mode 100644 LICENSE
create mode 100644 cram.mk
create mode 100644 ctest/.gitignore
create mode 100644 ctest/bamConcordant.t
delete mode 100644 ctest/bug25741.t
create mode 100644 ctest/cigarAdjecentIndels.t
create mode 100644 ctest/dataset.t
create mode 100644 ctest/deterministic.t
delete mode 100644 ctest/samNM.t
create mode 100644 ctest/unaligned.t
create mode 100644 debian/NEWS
create mode 100644 debian/patches/cmake-utils.patch
create mode 100644 debian/patches/disable-gtest.patch
delete mode 100644 extrautils/BasH5Simulator.cpp
delete mode 100644 extrautils/CCSH5ToBam.cpp
delete mode 100644 extrautils/ctest/alchemy.t
delete mode 100644 extrautils/ctest/ccsh5tobam.t
rename {include => iblasr}/BlasrAlign.hpp (67%)
rename {include => iblasr}/BlasrAlignImpl.hpp (93%)
create mode 100644 iblasr/BlasrHeaders.h
create mode 100644 iblasr/BlasrMiscs.hpp
rename {include => iblasr}/BlasrMiscsImpl.hpp (58%)
rename {include => iblasr}/BlasrUtils.hpp (76%)
rename {include => iblasr}/BlasrUtilsImpl.hpp (93%)
rename {include => iblasr}/MappingBuffers.hpp (54%)
rename {include => iblasr}/MappingIPC.h (86%)
rename {include => iblasr}/MappingParameters.h (76%)
rename {include => iblasr}/MappingSemaphores.h (75%)
rename {include => iblasr}/ReadAlignments.hpp (71%)
rename {include => iblasr}/RegisterBlasrOptions.h (60%)
rename {include => iblasr}/RegisterFilterOptions.h (56%)
delete mode 100644 include/BlasrHeaders.h
delete mode 100644 include/BlasrMiscs.hpp
create mode 100644 sub.mk
create mode 100644 utils/bam2bax/BUILD.txt
create mode 100644 utils/bam2bax/CMakeLists.txt
create mode 100644 utils/bam2bax/README.md
create mode 100644 utils/bam2bax/makefile
create mode 100644 utils/bam2bax/src/Bam2Bax.cpp
create mode 100644 utils/bam2bax/src/Bam2Bax.h
create mode 100644 utils/bam2bax/src/Bam2BaxConverter.h
create mode 100644 utils/bam2bax/src/Bam2BaxConverterImpl.hpp
create mode 100644 utils/bam2bax/src/Bam2BaxInternal.h
create mode 100644 utils/bam2bax/src/Bam2BaxMain.cpp
create mode 100644 utils/bam2bax/src/Bam2PlxMain.cpp
create mode 100644 utils/bam2bax/src/CMakeLists.txt
create mode 100644 utils/bam2bax/src/Converter.cpp
create mode 100644 utils/bam2bax/src/Converter.h
create mode 100644 utils/bam2bax/src/MetadataWriter.cpp
create mode 100644 utils/bam2bax/src/MetadataWriter.h
create mode 100644 utils/bam2bax/src/OptionParser.cpp
create mode 100644 utils/bam2bax/src/OptionParser.h
create mode 100644 utils/bam2bax/src/RegionTypeAdapter.h
create mode 100644 utils/bam2bax/src/RegionsAdapter.h
create mode 100644 utils/bam2bax/src/Settings.cpp
create mode 100644 utils/bam2bax/src/Settings.h
create mode 100644 utils/bam2bax/tests/CMakeLists.txt
create mode 100755 utils/bam2bax/tests/cram/bam2bax.t
create mode 100755 utils/bam2bax/tests/cram/bam2plx.t
create mode 100644 utils/bam2bax/tests/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.scraps.bam
create mode 100644 utils/bam2bax/tests/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.subreads.bam
create mode 100644 utils/bam2bax/tests/data/tiny.scraps.sam
create mode 100644 utils/bam2bax/tests/data/tiny.subreads.sam
create mode 100644 utils/bam2bax/tests/data/tiny_bam2plx.polymerase.sam
create mode 100755 utils/bam2bax/tests/example/end-to-end.sh
create mode 100644 utils/bam2bax/tests/files.cmake
create mode 100755 utils/bam2bax/tests/resequencing/bam2bax_resequencing.py
create mode 100755 utils/bam2bax/tests/resequencing/one_bax_test.sh
create mode 100755 utils/bam2bax/tests/resequencing/settings.xml
create mode 100755 utils/bam2bax/tests/resequencing/tiny_test.sh
create mode 100644 utils/bam2bax/tests/src/TestConstants.h
create mode 100644 utils/bam2bax/tests/src/TestData.h.in
create mode 100644 utils/bam2bax/tests/src/TestUtils.cpp
create mode 100644 utils/bam2bax/tests/src/TestUtils.h
create mode 100644 utils/bam2bax/tests/src/test.cpp
create mode 100644 utils/bam2bax/tests/src/test_Bam2BaxConverter.cpp
create mode 100644 utils/bam2bax/tests/src/test_HDFBaseCallsWriter.cpp
create mode 100644 utils/bam2bax/tests/src/test_HDFBaxWriter.cpp
create mode 100644 utils/bam2bax/tests/src/test_HDFScanDataWriter.cpp
create mode 100644 utils/bam2bax/tests/src/test_HDFZMWMetricsWriter.cpp
create mode 100644 utils/bam2bax/tests/src/test_HDFZMWWriter.cpp
create mode 100644 utils/bax2bam/BUILD.txt
create mode 100644 utils/bax2bam/CMakeLists.txt
create mode 100644 utils/bax2bam/README.md
create mode 100644 utils/bax2bam/makefile
create mode 100644 utils/bax2bam/src/Bax2Bam.cpp
create mode 100644 utils/bax2bam/src/Bax2Bam.h
create mode 100644 utils/bax2bam/src/CMakeLists.txt
create mode 100644 utils/bax2bam/src/CcsConverter.cpp
create mode 100644 utils/bax2bam/src/CcsConverter.h
create mode 100644 utils/bax2bam/src/ConverterBase.h
create mode 100644 utils/bax2bam/src/HqRegionConverter.cpp
create mode 100644 utils/bax2bam/src/HqRegionConverter.h
create mode 100644 utils/bax2bam/src/IConverter.cpp
create mode 100644 utils/bax2bam/src/IConverter.h
create mode 100644 utils/bax2bam/src/OptionParser.cpp
create mode 100644 utils/bax2bam/src/OptionParser.h
create mode 100644 utils/bax2bam/src/PolymeraseReadConverter.cpp
create mode 100644 utils/bax2bam/src/PolymeraseReadConverter.h
create mode 100644 utils/bax2bam/src/Settings.cpp
create mode 100644 utils/bax2bam/src/Settings.h
create mode 100644 utils/bax2bam/src/SubreadConverter.cpp
create mode 100644 utils/bax2bam/src/SubreadConverter.h
create mode 100644 utils/bax2bam/src/main.cpp
create mode 100644 utils/bax2bam/tests/CMakeLists.txt
create mode 100644 utils/bax2bam/tests/bax2bam.t
create mode 100644 utils/bax2bam/tests/files.cmake
create mode 100644 utils/bax2bam/tests/src/TestData.h.in
create mode 100644 utils/bax2bam/tests/src/TestUtils.cpp
create mode 100644 utils/bax2bam/tests/src/TestUtils.h
create mode 100644 utils/bax2bam/tests/src/test_ccs.cpp
create mode 100644 utils/bax2bam/tests/src/test_common.cpp
create mode 100644 utils/bax2bam/tests/src/test_hqregions.cpp
create mode 100644 utils/bax2bam/tests/src/test_polymerase.cpp
create mode 100644 utils/bax2bam/tests/src/test_subreads.cpp
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/fused-src/gtest/.deps/test_fused_gtest_test-gtest-all.Po
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/fused-src/gtest/.deps/test_fused_gtest_test-gtest_main.Po
copy debian/patches/series => utils/bax2bam/third-party/gtest-1.7.0/lib/.dirstamp (100%)
copy debian/patches/series => utils/bax2bam/third-party/gtest-1.7.0/samples/.deps/.dirstamp (100%)
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/samples/.deps/sample1.Plo
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/samples/.deps/sample10_unittest.Po
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/samples/.deps/sample1_unittest.Po
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/samples/.deps/sample2.Plo
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/samples/.deps/sample4.Plo
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/samples/.deps/test_fused_gtest_test-sample1.Po
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/samples/.deps/test_fused_gtest_test-sample1_unittest.Po
copy debian/patches/series => utils/bax2bam/third-party/gtest-1.7.0/samples/.dirstamp (100%)
copy debian/patches/series => utils/bax2bam/third-party/gtest-1.7.0/src/.deps/.dirstamp (100%)
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/src/.deps/gtest-all.Plo
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/src/.deps/gtest_main.Plo
copy debian/patches/series => utils/bax2bam/third-party/gtest-1.7.0/src/.dirstamp (100%)
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/test/.deps/gtest_all_test.Po
create mode 100644 utils/ctest/.gitignore
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.git
More information about the debian-med-commit
mailing list