[med-svn] [blasr] 02/13: Merge tag 'upstream/5.2'
Afif Elghraoui
afif at moszumanska.debian.org
Mon Oct 24 01:24:35 UTC 2016
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afif pushed a commit to branch master
in repository blasr.
commit b8aaf16a980797cdde23c968e068d0d407ddb5f6
Merge: 11817b4 9690aa9
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sun Jul 24 16:25:29 2016 -0700
Merge tag 'upstream/5.2'
Upstream version 5.2
.gitignore | 9 +
Blasr.cpp | 260 ++---
LICENSE | 34 +
README.INSTALL.md | 24 +-
configure.py | 10 +-
cram.mk | 34 +
ctest/.gitignore | 1 +
ctest/bamConcordant.t | 33 +
ctest/cigarAdjecentIndels.t | 22 +
ctest/concordant.t | 7 +-
ctest/dataset.t | 64 ++
ctest/deterministic.t | 47 +
ctest/filtercriteria.t | 2 +-
ctest/open_fail.t | 2 +-
ctest/setup.sh | 7 +-
ctest/unaligned.t | 25 +
ctest/useccsallBestN1.t | 4 +-
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 | 113 +++
iblasr/BlasrMiscs.hpp | 62 ++
{include => iblasr}/BlasrMiscsImpl.hpp | 100 +-
{include => iblasr}/BlasrUtils.hpp | 50 +-
{include => iblasr}/BlasrUtilsImpl.hpp | 100 +-
{include => iblasr}/MappingBuffers.hpp | 52 +-
{include => iblasr}/MappingIPC.h | 30 +-
{include => iblasr}/MappingParameters.h | 89 +-
{include => iblasr}/MappingSemaphores.h | 15 +-
{include => iblasr}/ReadAlignments.hpp | 45 +-
{include => iblasr}/RegisterBlasrOptions.h | 402 ++++----
{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 | 54 +-
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 | 29 +
utils/bam2bax/src/Bam2Bax.cpp | 29 +
utils/bam2bax/src/Bam2Bax.h | 13 +
utils/bam2bax/src/Bam2BaxConverter.h | 38 +
utils/bam2bax/src/Bam2BaxConverterImpl.hpp | 71 ++
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 | 146 +++
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 | 232 +++++
utils/bam2bax/src/Settings.h | 80 ++
utils/bam2bax/tests/CMakeLists.txt | 93 ++
utils/bam2bax/tests/cram/bam2bax.t | 86 ++
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 | 128 +++
utils/bax2bam/README.md | 62 ++
utils/bax2bam/makefile | 29 +
utils/bax2bam/src/Bax2Bam.cpp | 191 ++++
utils/bax2bam/src/Bax2Bam.h | 13 +
utils/bax2bam/src/CMakeLists.txt | 57 ++
utils/bax2bam/src/CcsConverter.cpp | 117 +++
utils/bax2bam/src/CcsConverter.h | 47 +
utils/bax2bam/src/ConverterBase.h | 1019 ++++++++++++++++++++
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 | 261 +++++
utils/bax2bam/src/Settings.h | 87 ++
utils/bax2bam/src/SubreadConverter.cpp | 395 ++++++++
utils/bax2bam/src/SubreadConverter.h | 26 +
utils/bax2bam/src/main.cpp | 118 +++
utils/bax2bam/tests/CMakeLists.txt | 88 ++
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 | 421 ++++++++
utils/bax2bam/tests/src/test_polymerase.cpp | 236 +++++
utils/bax2bam/tests/src/test_subreads.cpp | 410 ++++++++
.../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/makefile | 22 +-
152 files changed, 12135 insertions(+), 2149 deletions(-)
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