[med-svn] [blasr] branch upstream updated (b282ecd -> 317d7eb)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Oct 24 01:24:36 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository blasr.
from b282ecd Imported Upstream version 0~20151014+git8e668be
new 9690aa9 Imported Upstream version 5.2
new 317d7eb Imported Upstream version 5.3
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 | 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 +-
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 +-
173 files changed, 12368 insertions(+), 2293 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
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
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/lib/.dirstamp
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/samples/.deps/.dirstamp
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
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/samples/.dirstamp
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/src/.deps/.dirstamp
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
create mode 100644 utils/bax2bam/third-party/gtest-1.7.0/src/.dirstamp
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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