[med-svn] [blasr] branch master updated (11817b4 -> c441dc6)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Oct 24 01:24:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository blasr.
from 11817b4 blasr (0~20151014+git8e668be-1) unstable; urgency=high
new 9690aa9 Imported Upstream version 5.2
new b8aaf16 Merge tag 'upstream/5.2'
new 3a18309 Find PB libraries in the default LD path
new 3d5b72b Bump Standards-Version to 3.9.8
new 763ecfe Use encrypted protocols for VCS
new 3a12f90 Update email address and copyright year
new 317d7eb Imported Upstream version 5.3
new 0fc2023 Merge tag 'upstream/5.3'
new 0eeb861 Update paths to pbseqlib headers
new 29cad32 Remove unused lintian overrides
new 38c3d4f Update debian/TODO
new 53c26a4 Add d/NEWS to explain interface change
new c441dc6 d/rules: Minor clean-ups
The 13 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 | 39 +
ctest/.gitignore | 1 +
ctest/affineAlign.t | 6 +-
ctest/aggressiveIntervalCut.t | 4 +-
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 | 17 +-
ctest/dataset.t | 64 ++
ctest/deterministic.t | 47 +
ctest/ecoli.t | 10 +-
ctest/fastMaxInterval.t | 4 +-
ctest/filtercriteria.t | 8 +-
ctest/fofn.t | 4 +-
ctest/hitpolicy.t | 18 +-
ctest/holeNumbers.t | 4 +-
ctest/m0-5.t | 10 +-
ctest/multipart.t | 2 +-
ctest/noSplitSubreads.t | 6 +-
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 | 7 +-
debian/control | 8 +-
debian/copyright | 4 +-
debian/lintian-overrides | 4 -
debian/rules | 14 +-
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 | 134 ++-
{include => iblasr}/MappingSemaphores.h | 15 +-
{include => iblasr}/ReadAlignments.hpp | 45 +-
{include => iblasr}/RegisterBlasrOptions.h | 412 ++++----
{include => iblasr}/RegisterFilterOptions.h | 41 +-
include/BlasrHeaders.h | 149 ---
include/BlasrMiscs.hpp | 100 --
makefile | 36 +-
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 | 48 +
utils/bam2bax/CMakeLists.txt | 133 +++
utils/bam2bax/README.md | 11 +
utils/bam2bax/makefile | 30 +
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 | 79 ++
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 | 93 ++
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 | 130 +++
utils/bax2bam/README.md | 62 ++
utils/bax2bam/makefile | 30 +
utils/bax2bam/src/Bax2Bam.cpp | 251 +++++
utils/bax2bam/src/Bax2Bam.h | 13 +
utils/bax2bam/src/CMakeLists.txt | 59 ++
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 | 85 ++
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 | 89 ++
utils/bax2bam/tests/bax2bam.t | 7 +
utils/bax2bam/tests/files.cmake | 52 +
utils/bax2bam/tests/src/TestData.h.in | 17 +
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 +-
179 files changed, 12390 insertions(+), 2314 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
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 (80%)
rename {include => iblasr}/MappingSemaphores.h (75%)
rename {include => iblasr}/ReadAlignments.hpp (71%)
rename {include => iblasr}/RegisterBlasrOptions.h (61%)
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
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