[med-svn] [manta] branch upstream updated (bbe60d4 -> a245490)
Andreas Tille
tille at debian.org
Tue May 2 12:34:06 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository manta.
from bbe60d4 New upstream version 1.0.2+dfsg
new a245490 New upstream version 1.1.0+dfsg
The 1 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:
CMakeLists.txt | 2 +-
COPYRIGHT.txt | 4 +-
ChangeLog.txt | 19 +
docs/developerGuide/README.md | 8 +-
docs/developerGuide/alignment.md | 8 +-
docs/developerGuide/breakendGraph.md | 8 +-
docs/developerGuide/debugFullRun.md | 8 +-
docs/developerGuide/debugSingleSV.md | 8 +-
docs/developerGuide/testAssembler.md | 8 +-
docs/methods/primary/methods.tex | 149 ++++++--
docs/userGuide/README.md | 17 +-
docs/userGuide/installation.md | 18 +-
redist/CMakeLists.txt | 2 +-
src/CMakeLists.txt | 2 +-
src/c++/CMakeLists.txt | 2 +-
src/c++/bin/CMakeLists.txt | 2 +-
src/c++/bin/CheckSVLoci.cpp | 3 +-
src/c++/bin/DumpSVLoci.cpp | 3 +-
src/c++/bin/EstimateSVLoci.cpp | 3 +-
src/c++/bin/GenerateSVCandidates.cpp | 3 +-
src/c++/bin/GetAlignmentStats.cpp | 3 +-
src/c++/bin/GetChromDepth.cpp | 3 +-
src/c++/bin/MergeAlignmentStats.cpp | 3 +-
src/c++/bin/MergeEdgeStats.cpp | 3 +-
src/c++/bin/MergeSVLoci.cpp | 3 +-
src/c++/bin/SummarizeAlignmentStats.cpp | 3 +-
src/c++/bin/SummarizeSVLoci.cpp | 3 +-
src/c++/bin/TestAssembler.cpp | 3 +-
src/c++/lib/CMakeLists.txt | 2 +-
src/c++/lib/alignment/AlignerBase.hh | 3 +-
src/c++/lib/alignment/AlignerBaseImpl.hh | 3 +-
src/c++/lib/alignment/AlignerUtil.hh | 3 +-
src/c++/lib/alignment/Alignment.cpp | 3 +-
src/c++/lib/alignment/Alignment.hh | 3 +-
src/c++/lib/alignment/AlignmentScores.hh | 3 +-
src/c++/lib/alignment/AlignmentUtil.cpp | 3 +-
src/c++/lib/alignment/AlignmentUtil.hh | 3 +-
src/c++/lib/alignment/CMakeLists.txt | 2 +-
src/c++/lib/alignment/GlobalAligner.hh | 3 +-
src/c++/lib/alignment/GlobalAlignerImpl.hh | 3 +-
src/c++/lib/alignment/GlobalJumpAligner.hh | 3 +-
src/c++/lib/alignment/GlobalJumpAlignerImpl.hh | 3 +-
src/c++/lib/alignment/GlobalJumpIntronAligner.hh | 3 +-
.../lib/alignment/GlobalJumpIntronAlignerImpl.hh | 3 +-
src/c++/lib/alignment/GlobalLargeIndelAligner.hh | 3 +-
.../lib/alignment/GlobalLargeIndelAlignerImpl.hh | 3 +-
src/c++/lib/alignment/JumpAlignerBase.hh | 3 +-
src/c++/lib/alignment/JumpAlignerBaseImpl.hh | 3 +-
src/c++/lib/alignment/ReadScorer.cpp | 3 +-
src/c++/lib/alignment/ReadScorer.hh | 3 +-
src/c++/lib/alignment/SingleRefAlignerShared.hh | 3 +-
.../lib/alignment/SingleRefAlignerSharedImpl.hh | 3 +-
src/c++/lib/alignment/test/AlignmentUtilTest.cpp | 3 +-
src/c++/lib/alignment/test/CMakeLists.txt | 2 +-
src/c++/lib/alignment/test/GlobalAlignerTest.cpp | 3 +-
.../lib/alignment/test/GlobalJumpAlignerTest.cpp | 3 +-
.../alignment/test/GlobalJumpIntronAlignerTest.cpp | 3 +-
.../alignment/test/GlobalLargeIndelAlignerTest.cpp | 3 +-
src/c++/lib/alignment/test/test_main.cpp | 3 +-
src/c++/lib/applications/CMakeLists.txt | 2 +-
.../lib/applications/CheckSVLoci/CMakeLists.txt | 2 +-
.../lib/applications/CheckSVLoci/CSLOptions.cpp | 3 +-
src/c++/lib/applications/CheckSVLoci/CSLOptions.hh | 3 +-
.../lib/applications/CheckSVLoci/CheckSVLoci.cpp | 3 +-
.../lib/applications/CheckSVLoci/CheckSVLoci.hh | 3 +-
src/c++/lib/applications/DumpSVLoci/CMakeLists.txt | 2 +-
src/c++/lib/applications/DumpSVLoci/DSLOptions.cpp | 3 +-
src/c++/lib/applications/DumpSVLoci/DSLOptions.hh | 3 +-
src/c++/lib/applications/DumpSVLoci/DumpSVLoci.cpp | 3 +-
src/c++/lib/applications/DumpSVLoci/DumpSVLoci.hh | 3 +-
.../lib/applications/EstimateSVLoci/CMakeLists.txt | 2 +-
.../lib/applications/EstimateSVLoci/ESLOptions.cpp | 5 +-
.../lib/applications/EstimateSVLoci/ESLOptions.hh | 4 +-
.../applications/EstimateSVLoci/EstimateSVLoci.cpp | 3 +-
.../applications/EstimateSVLoci/EstimateSVLoci.hh | 3 +-
.../EstimateSVLoci/SVLocusSetFinder.cpp | 3 +-
.../EstimateSVLoci/SVLocusSetFinder.hh | 3 +-
.../GenerateSVCandidates/CMakeLists.txt | 2 +-
.../GenerateSVCandidates/EdgeOptions.hh | 3 +-
.../GenerateSVCandidates/EdgeOptionsParser.cpp | 3 +-
.../GenerateSVCandidates/EdgeOptionsParser.hh | 3 +-
.../GenerateSVCandidates/EdgeRetriever.hh | 3 +-
.../GenerateSVCandidates/EdgeRetrieverBin.cpp | 3 +-
.../GenerateSVCandidates/EdgeRetrieverBin.hh | 3 +-
.../GenerateSVCandidates/EdgeRetrieverJumpBin.cpp | 3 +-
.../GenerateSVCandidates/EdgeRetrieverJumpBin.hh | 3 +-
.../GenerateSVCandidates/EdgeRetrieverLocus.cpp | 3 +-
.../GenerateSVCandidates/EdgeRetrieverLocus.hh | 3 +-
.../GenerateSVCandidates/EdgeRuntimeTracker.cpp | 3 +-
.../GenerateSVCandidates/EdgeRuntimeTracker.hh | 3 +-
.../GenerateSVCandidates/FatSVCandidate.cpp | 3 +-
.../GenerateSVCandidates/FatSVCandidate.hh | 3 +-
.../GenerateSVCandidates/GSCEdgeStatsManager.cpp | 3 +-
.../GenerateSVCandidates/GSCEdgeStatsManager.hh | 5 +-
.../GenerateSVCandidates/GSCOptions.cpp | 5 +-
.../GenerateSVCandidates/GSCOptions.hh | 6 +-
.../GenerateSVCandidates/GenerateSVCandidates.cpp | 6 +-
.../GenerateSVCandidates/GenerateSVCandidates.hh | 3 +-
.../GenerateSVCandidates/JunctionCallInfo.hh | 3 +-
.../SVCandidateAssemblyRefiner.cpp | 3 +-
.../SVCandidateAssemblyRefiner.hh | 3 +-
.../GenerateSVCandidates/SVCandidateProcessor.cpp | 148 ++++++--
.../GenerateSVCandidates/SVCandidateProcessor.hh | 4 +-
.../GenerateSVCandidates/SVEvidence.cpp | 3 +-
.../GenerateSVCandidates/SVEvidence.hh | 3 +-
.../applications/GenerateSVCandidates/SVFinder.cpp | 15 +-
.../applications/GenerateSVCandidates/SVFinder.hh | 8 +-
.../SVScorePairAltProcessor.cpp | 3 +-
.../SVScorePairAltProcessor.hh | 3 +-
.../GenerateSVCandidates/SVScorePairProcessor.cpp | 3 +-
.../GenerateSVCandidates/SVScorePairProcessor.hh | 15 +-
.../SVScorePairRefProcessor.cpp | 12 +-
.../SVScorePairRefProcessor.hh | 3 +-
.../applications/GenerateSVCandidates/SVScorer.cpp | 70 ++--
.../applications/GenerateSVCandidates/SVScorer.hh | 20 +-
.../GenerateSVCandidates/SVScorerPair.cpp | 12 +-
.../GenerateSVCandidates/SVScorerPairOptions.hh | 15 +-
.../GenerateSVCandidates/SVScorerShared.cpp | 3 +-
.../GenerateSVCandidates/SVScorerShared.hh | 3 +-
.../GenerateSVCandidates/SVScorerSplit.cpp | 11 +-
.../GenerateSVCandidates/SVSupports.cpp | 9 +-
.../GenerateSVCandidates/SVSupports.hh | 7 +-
.../GenerateSVCandidates/SplitReadAlignment.cpp | 3 +-
.../GenerateSVCandidates/SplitReadAlignment.hh | 3 +-
.../GenerateSVCandidates/test/CMakeLists.txt | 2 +-
.../test/EdgeRetrieverBinTest.cpp | 3 +-
.../test/EdgeRetrieverJumpBinTest.cpp | 3 +-
.../test/EdgeRetrieverLocusTest.cpp | 3 +-
.../test/SVCandidateAssemblyRefinerTest.cpp | 3 +-
.../GenerateSVCandidates/test/test_main.cpp | 3 +-
.../GetAlignmentStats/AlignmentStatsOptions.cpp | 3 +-
.../GetAlignmentStats/AlignmentStatsOptions.hh | 3 +-
.../applications/GetAlignmentStats/CMakeLists.txt | 2 +-
.../GetAlignmentStats/GetAlignmentStats.cpp | 3 +-
.../GetAlignmentStats/GetAlignmentStats.hh | 3 +-
.../lib/applications/GetChromDepth/CMakeLists.txt | 2 +-
.../GetChromDepth/ChromDepthOptions.cpp | 3 +-
.../GetChromDepth/ChromDepthOptions.hh | 3 +-
.../applications/GetChromDepth/GetChromDepth.cpp | 3 +-
.../applications/GetChromDepth/GetChromDepth.hh | 3 +-
.../MergeAlignmentStats/CMakeLists.txt | 2 +-
.../MergeAlignmentStats/MergeAlignmentStats.cpp | 3 +-
.../MergeAlignmentStats/MergeAlignmentStats.hh | 3 +-
.../MergeAlignmentStatsOptions.cpp | 3 +-
.../MergeAlignmentStatsOptions.hh | 3 +-
.../lib/applications/MergeEdgeStats/CMakeLists.txt | 2 +-
.../lib/applications/MergeEdgeStats/MESOptions.cpp | 3 +-
.../lib/applications/MergeEdgeStats/MESOptions.hh | 3 +-
.../applications/MergeEdgeStats/MergeEdgeStats.cpp | 3 +-
.../applications/MergeEdgeStats/MergeEdgeStats.hh | 3 +-
.../lib/applications/MergeSVLoci/CMakeLists.txt | 2 +-
.../lib/applications/MergeSVLoci/MSLOptions.cpp | 3 +-
src/c++/lib/applications/MergeSVLoci/MSLOptions.hh | 3 +-
.../lib/applications/MergeSVLoci/MergeSVLoci.cpp | 3 +-
.../lib/applications/MergeSVLoci/MergeSVLoci.hh | 3 +-
.../SummarizeAlignmentStats/CMakeLists.txt | 2 +-
.../SummarizeAlignmentStats/SASOptions.cpp | 3 +-
.../SummarizeAlignmentStats/SASOptions.hh | 3 +-
.../SummarizeAlignmentStats.cpp | 14 +-
.../SummarizeAlignmentStats.hh | 3 +-
.../applications/SummarizeSVLoci/CMakeLists.txt | 2 +-
.../applications/SummarizeSVLoci/SSLOptions.cpp | 3 +-
.../lib/applications/SummarizeSVLoci/SSLOptions.hh | 3 +-
.../SummarizeSVLoci/SummarizeSVLoci.cpp | 3 +-
.../SummarizeSVLoci/SummarizeSVLoci.hh | 3 +-
.../lib/applications/TestAssembler/CMakeLists.txt | 2 +-
.../applications/TestAssembler/TestAssembler.cpp | 3 +-
.../applications/TestAssembler/TestAssembler.hh | 3 +-
.../TestAssembler/TestAssemblerOptions.cpp | 3 +-
.../TestAssembler/TestAssemblerOptions.hh | 3 +-
.../TestAssembler/extractAssemblyReads.cpp | 3 +-
.../TestAssembler/extractAssemblyReads.hh | 3 +-
src/c++/lib/appstats/CMakeLists.txt | 2 +-
src/c++/lib/appstats/GSCEdgeStats.cpp | 3 +-
src/c++/lib/appstats/GSCEdgeStats.hh | 3 +-
src/c++/lib/appstats/SVFinderStats.cpp | 3 +-
src/c++/lib/appstats/SVFinderStats.hh | 19 +-
src/c++/lib/assembly/AssembledContig.cpp | 3 +-
src/c++/lib/assembly/AssembledContig.hh | 3 +-
src/c++/lib/assembly/AssemblyReadInfo.hh | 3 +-
src/c++/lib/assembly/CMakeLists.txt | 2 +-
src/c++/lib/assembly/IterativeAssembler.cpp | 3 +-
src/c++/lib/assembly/IterativeAssembler.hh | 3 +-
src/c++/lib/assembly/SmallAssembler.cpp | 3 +-
src/c++/lib/assembly/SmallAssembler.hh | 3 +-
src/c++/lib/assembly/test/CMakeLists.txt | 2 +-
.../lib/assembly/test/IterativeAssemblerTest.cpp | 3 +-
src/c++/lib/assembly/test/SmallAssemblerTest.cpp | 3 +-
src/c++/lib/assembly/test/test_main.cpp | 3 +-
src/c++/lib/blt_util/CMakeLists.txt | 2 +-
src/c++/lib/blt_util/CircularCounter.hh | 3 +-
src/c++/lib/blt_util/LinearScaler.hh | 3 +-
src/c++/lib/blt_util/MedianDepthTracker.hh | 3 +-
src/c++/lib/blt_util/PolymorphicObject.hh | 3 +-
src/c++/lib/blt_util/RangeMap.hh | 3 +-
src/c++/lib/blt_util/ReadKey.cpp | 3 +-
src/c++/lib/blt_util/ReadKey.hh | 3 +-
src/c++/lib/blt_util/RegionSum.hh | 3 +-
src/c++/lib/blt_util/RegionTracker.cpp | 3 +-
src/c++/lib/blt_util/RegionTracker.hh | 9 +-
src/c++/lib/blt_util/RegionTrackerImpl.hh | 3 +-
src/c++/lib/blt_util/SampleVector.hh | 3 +-
src/c++/lib/blt_util/SampleVectorImpl.hh | 3 +-
src/c++/lib/blt_util/SimpleAlignment.cpp | 3 +-
src/c++/lib/blt_util/SimpleAlignment.hh | 3 +-
src/c++/lib/blt_util/SizeDistribution.cpp | 3 +-
src/c++/lib/blt_util/SizeDistribution.hh | 3 +-
src/c++/lib/blt_util/align_path.cpp | 3 +-
src/c++/lib/blt_util/align_path.hh | 3 +-
src/c++/lib/blt_util/align_path_impl.hh | 3 +-
.../lib/blt_util/align_path_match_descriptor.cpp | 3 +-
.../lib/blt_util/align_path_match_descriptor.hh | 3 +-
src/c++/lib/blt_util/align_path_util.hh | 3 +-
src/c++/lib/blt_util/basic_matrix.hh | 3 +-
src/c++/lib/blt_util/binomial_test.cpp | 3 +-
src/c++/lib/blt_util/binomial_test.hh | 3 +-
src/c++/lib/blt_util/blt_exception.cpp | 3 +-
src/c++/lib/blt_util/blt_exception.hh | 3 +-
src/c++/lib/blt_util/blt_types.hh | 3 +-
src/c++/lib/blt_util/chrom_depth_map.cpp | 3 +-
src/c++/lib/blt_util/chrom_depth_map.hh | 3 +-
src/c++/lib/blt_util/compat_unistd.h | 2 +-
src/c++/lib/blt_util/compat_util.cpp | 3 +-
src/c++/lib/blt_util/compat_util.hh | 3 +-
src/c++/lib/blt_util/depth_buffer.hh | 3 +-
src/c++/lib/blt_util/depth_buffer_util.cpp | 3 +-
src/c++/lib/blt_util/depth_buffer_util.hh | 3 +-
src/c++/lib/blt_util/flyweight_observer.hh | 3 +-
src/c++/lib/blt_util/id_map.hh | 3 +-
src/c++/lib/blt_util/input_stream_handler.cpp | 3 +-
src/c++/lib/blt_util/input_stream_handler.hh | 3 +-
src/c++/lib/blt_util/io_util.cpp | 3 +-
src/c++/lib/blt_util/io_util.hh | 3 +-
src/c++/lib/blt_util/istream_line_splitter.cpp | 3 +-
src/c++/lib/blt_util/istream_line_splitter.hh | 3 +-
src/c++/lib/blt_util/known_pos_range2.cpp | 3 +-
src/c++/lib/blt_util/known_pos_range2.hh | 10 +-
src/c++/lib/blt_util/log.cpp | 3 +-
src/c++/lib/blt_util/log.hh | 3 +-
src/c++/lib/blt_util/math_util.hh | 3 +-
src/c++/lib/blt_util/observer.hh | 3 +-
src/c++/lib/blt_util/parse_util.cpp | 3 +-
src/c++/lib/blt_util/parse_util.hh | 3 +-
src/c++/lib/blt_util/pos_processor_base.hh | 3 +-
src/c++/lib/blt_util/pos_range.cpp | 3 +-
src/c++/lib/blt_util/pos_range.hh | 27 +-
src/c++/lib/blt_util/prob_util.cpp | 3 +-
src/c++/lib/blt_util/prob_util.hh | 40 +-
src/c++/lib/blt_util/qscore.hh | 6 +-
src/c++/lib/blt_util/qscore_cache.cpp | 3 +-
src/c++/lib/blt_util/qscore_cache.hh | 3 +-
src/c++/lib/blt_util/qscore_snp.cpp | 3 +-
src/c++/lib/blt_util/qscore_snp.hh | 3 +-
src/c++/lib/blt_util/reference_contig_segment.hh | 3 +-
src/c++/lib/blt_util/seq_printer.cpp | 3 +-
src/c++/lib/blt_util/seq_printer.hh | 3 +-
src/c++/lib/blt_util/seq_util.cpp | 3 +-
src/c++/lib/blt_util/seq_util.hh | 3 +-
src/c++/lib/blt_util/set_util.hh | 3 +-
src/c++/lib/blt_util/sig_handler.cpp | 3 +-
src/c++/lib/blt_util/sig_handler.hh | 3 +-
src/c++/lib/blt_util/stage_manager.cpp | 3 +-
src/c++/lib/blt_util/stage_manager.hh | 3 +-
src/c++/lib/blt_util/stat_util.cpp | 3 +-
src/c++/lib/blt_util/stat_util.hh | 3 +-
src/c++/lib/blt_util/stream_stat.cpp | 3 +-
src/c++/lib/blt_util/stream_stat.hh | 3 +-
src/c++/lib/blt_util/string_util.cpp | 3 +-
src/c++/lib/blt_util/string_util.hh | 3 +-
src/c++/lib/blt_util/test/CMakeLists.txt | 2 +-
src/c++/lib/blt_util/test/CircularCounter_test.cpp | 3 +-
.../lib/blt_util/test/MedianDepthTracker_test.cpp | 3 +-
src/c++/lib/blt_util/test/RangeMap_test.cpp | 3 +-
src/c++/lib/blt_util/test/RegionSum_test.cpp | 3 +-
src/c++/lib/blt_util/test/RegionTracker_test.cpp | 3 +-
src/c++/lib/blt_util/test/SampleVector_test.cpp | 3 +-
src/c++/lib/blt_util/test/SimpleAlignment_test.cpp | 3 +-
.../lib/blt_util/test/SizeDistribution_test.cpp | 3 +-
src/c++/lib/blt_util/test/align_path_test.cpp | 7 +-
src/c++/lib/blt_util/test/binomial_test_test.cpp | 3 +-
src/c++/lib/blt_util/test/boost_icl_test.cpp | 3 +-
src/c++/lib/blt_util/test/compat_util_test.cpp | 3 +-
src/c++/lib/blt_util/test/depth_buffer_test.cpp | 3 +-
src/c++/lib/blt_util/test/id_map_test.cpp | 3 +-
src/c++/lib/blt_util/test/io_util_test.cpp | 3 +-
.../blt_util/test/istream_line_splitter_test.cpp | 3 +-
.../lib/blt_util/test/known_pos_range2_test.cpp | 3 +-
src/c++/lib/blt_util/test/math_util_test.cpp | 3 +-
src/c++/lib/blt_util/test/observer_test.cpp | 3 +-
src/c++/lib/blt_util/test/parse_util_test.cpp | 3 +-
src/c++/lib/blt_util/test/pos_range_test.cpp | 3 +-
src/c++/lib/blt_util/test/prob_util_test.cpp | 3 +-
src/c++/lib/blt_util/test/seq_util_test.cpp | 3 +-
src/c++/lib/blt_util/test/set_util_test.cpp | 3 +-
src/c++/lib/blt_util/test/stage_manager_test.cpp | 3 +-
src/c++/lib/blt_util/test/stream_stat_test.cpp | 3 +-
src/c++/lib/blt_util/test/string_util_test.cpp | 3 +-
src/c++/lib/blt_util/test/test_main.cpp | 3 +-
src/c++/lib/blt_util/test/window_util_test.cpp | 3 +-
src/c++/lib/blt_util/thirdparty_pop.h | 3 +-
src/c++/lib/blt_util/thirdparty_push.h | 3 +-
src/c++/lib/blt_util/time_util.cpp | 3 +-
src/c++/lib/blt_util/time_util.hh | 3 +-
src/c++/lib/blt_util/window_util.hh | 7 +-
src/c++/lib/common/CMakeLists.txt | 2 +-
src/c++/lib/common/Exceptions.cpp | 3 +-
src/c++/lib/common/Exceptions.hh | 3 +-
src/c++/lib/common/OutStream.cpp | 3 +-
src/c++/lib/common/OutStream.hh | 3 +-
src/c++/lib/common/Program.cpp | 3 +-
src/c++/lib/common/Program.hh | 3 +-
src/c++/lib/common/ProgramConfig.hh | 3 +-
src/c++/lib/common/ProgramUtil.cpp | 3 +-
src/c++/lib/common/ProgramUtil.hh | 3 +-
src/c++/lib/common/ReadPairOrient.cpp | 3 +-
src/c++/lib/common/ReadPairOrient.hh | 3 +-
src/c++/lib/common/config.h.in | 3 +-
src/c++/lib/common/configBuildTimeInfo.h.in | 3 +-
src/c++/lib/common/test/CMakeLists.txt | 2 +-
src/c++/lib/common/test/ReadPairOrientTest.cpp | 3 +-
src/c++/lib/common/test/test_main.cpp | 3 +-
src/c++/lib/format/CMakeLists.txt | 2 +-
src/c++/lib/format/VcfWriterCandidateSV.cpp | 3 +-
src/c++/lib/format/VcfWriterCandidateSV.hh | 3 +-
src/c++/lib/format/VcfWriterDiploidSV.cpp | 3 +-
src/c++/lib/format/VcfWriterDiploidSV.hh | 3 +-
src/c++/lib/format/VcfWriterSV.cpp | 3 +-
src/c++/lib/format/VcfWriterSV.hh | 3 +-
src/c++/lib/format/VcfWriterScoredSV.hh | 3 +-
src/c++/lib/format/VcfWriterSomaticSV.cpp | 3 +-
src/c++/lib/format/VcfWriterSomaticSV.hh | 3 +-
src/c++/lib/format/VcfWriterTumorSV.cpp | 3 +-
src/c++/lib/format/VcfWriterTumorSV.hh | 3 +-
src/c++/lib/htsapi/CMakeLists.txt | 2 +-
src/c++/lib/htsapi/SimpleAlignment_bam_util.cpp | 3 +-
src/c++/lib/htsapi/SimpleAlignment_bam_util.hh | 3 +-
src/c++/lib/htsapi/align_path_bam_util.cpp | 3 +-
src/c++/lib/htsapi/align_path_bam_util.hh | 3 +-
src/c++/lib/htsapi/bam_dumper.cpp | 3 +-
src/c++/lib/htsapi/bam_dumper.hh | 3 +-
src/c++/lib/htsapi/bam_header_info.cpp | 3 +-
src/c++/lib/htsapi/bam_header_info.hh | 3 +-
src/c++/lib/htsapi/bam_header_util.cpp | 3 +-
src/c++/lib/htsapi/bam_header_util.hh | 10 +-
src/c++/lib/htsapi/bam_record.cpp | 8 +-
src/c++/lib/htsapi/bam_record.hh | 3 +-
src/c++/lib/htsapi/bam_record_util.cpp | 7 +-
src/c++/lib/htsapi/bam_record_util.hh | 3 +-
src/c++/lib/htsapi/bam_seq.cpp | 3 +-
src/c++/lib/htsapi/bam_seq.hh | 3 +-
src/c++/lib/htsapi/bam_seq_read_util.cpp | 3 +-
src/c++/lib/htsapi/bam_seq_read_util.hh | 3 +-
src/c++/lib/htsapi/bam_streamer.cpp | 35 +-
src/c++/lib/htsapi/bam_streamer.hh | 28 +-
src/c++/lib/htsapi/bam_util.cpp | 3 +-
src/c++/lib/htsapi/bam_util.hh | 3 +-
src/c++/lib/htsapi/bed_record.cpp | 3 +-
src/c++/lib/htsapi/bed_record.hh | 3 +-
src/c++/lib/htsapi/bed_streamer.cpp | 3 +-
src/c++/lib/htsapi/bed_streamer.hh | 13 +-
src/c++/lib/htsapi/hts_streamer.cpp | 26 +-
src/c++/lib/htsapi/hts_streamer.hh | 15 +-
src/c++/lib/htsapi/sam_util.hh | 3 +-
src/c++/lib/htsapi/samtools_fasta_util.cpp | 3 +-
src/c++/lib/htsapi/samtools_fasta_util.hh | 3 +-
src/c++/lib/htsapi/tabix_util.hh | 3 +-
src/c++/lib/htsapi/test/CMakeLists.txt | 2 +-
.../lib/htsapi/test/align_path_bam_util_test.cpp | 3 +-
src/c++/lib/htsapi/test/bam_header_util_test.cpp | 3 +-
src/c++/lib/htsapi/test/bed_streamer_test.cpp | 3 +-
src/c++/lib/htsapi/test/test_config.h.in | 3 +-
src/c++/lib/htsapi/test/test_main.cpp | 3 +-
src/c++/lib/htsapi/test/vcf_streamer_test.cpp | 182 ++++++++-
src/c++/lib/htsapi/test/vcf_streamer_test.vcf.gz | Bin 1126 -> 1898 bytes
.../lib/htsapi/test/vcf_streamer_test.vcf.gz.tbi | Bin 139 -> 273 bytes
src/c++/lib/htsapi/vcf_record.cpp | 17 +-
src/c++/lib/htsapi/vcf_record.hh | 29 +-
src/c++/lib/htsapi/vcf_streamer.cpp | 46 ++-
src/c++/lib/htsapi/vcf_streamer.hh | 35 +-
src/c++/lib/htsapi/vcf_util.cpp | 3 +-
src/c++/lib/htsapi/vcf_util.hh | 16 +-
src/c++/lib/manta/BamRegionProcessor.hh | 3 +-
src/c++/lib/manta/CMakeLists.txt | 2 +-
src/c++/lib/manta/ChromDepthFilterUtil.cpp | 3 +-
src/c++/lib/manta/ChromDepthFilterUtil.hh | 3 +-
src/c++/lib/manta/EventInfo.hh | 3 +-
src/c++/lib/manta/JunctionIdGenerator.cpp | 3 +-
src/c++/lib/manta/JunctionIdGenerator.hh | 5 +-
src/c++/lib/manta/MultiJunctionUtil.cpp | 49 ++-
src/c++/lib/manta/MultiJunctionUtil.hh | 15 +-
src/c++/lib/manta/ReadChromDepthUtil.cpp | 5 +-
src/c++/lib/manta/ReadChromDepthUtil.hh | 3 +-
src/c++/lib/manta/ReadGroupLabel.cpp | 3 +-
src/c++/lib/manta/ReadGroupLabel.hh | 3 +-
src/c++/lib/manta/ReadGroupStats.hh | 3 +-
src/c++/lib/manta/ReadGroupStatsSet.cpp | 3 +-
src/c++/lib/manta/ReadGroupStatsSet.hh | 3 +-
src/c++/lib/manta/ReadGroupStatsUtil.cpp | 405 +++++++++++++++++----
src/c++/lib/manta/ReadGroupStatsUtil.hh | 3 +-
src/c++/lib/manta/RemoteMateReadUtil.cpp | 3 +-
src/c++/lib/manta/RemoteMateReadUtil.hh | 3 +-
src/c++/lib/manta/SVBreakend.cpp | 3 +-
src/c++/lib/manta/SVBreakend.hh | 3 +-
src/c++/lib/manta/SVCandidate.cpp | 3 +-
src/c++/lib/manta/SVCandidate.hh | 12 +-
src/c++/lib/manta/SVCandidateAssembler.cpp | 7 +-
src/c++/lib/manta/SVCandidateAssembler.hh | 3 +-
src/c++/lib/manta/SVCandidateAssemblyData.cpp | 3 +-
src/c++/lib/manta/SVCandidateAssemblyData.hh | 3 +-
src/c++/lib/manta/SVCandidateSetData.cpp | 3 +-
src/c++/lib/manta/SVCandidateSetData.hh | 3 +-
src/c++/lib/manta/SVCandidateUtil.cpp | 5 +-
src/c++/lib/manta/SVCandidateUtil.hh | 3 +-
src/c++/lib/manta/SVLocusEvidenceCount.hh | 5 +-
src/c++/lib/manta/SVLocusScanner.cpp | 127 +++++--
src/c++/lib/manta/SVLocusScanner.hh | 10 +-
src/c++/lib/manta/SVLocusScannerSemiAligned.cpp | 3 +-
src/c++/lib/manta/SVLocusScannerSemiAligned.hh | 3 +-
src/c++/lib/manta/SVModelScoreInfo.hh | 3 +-
src/c++/lib/manta/SVMultiJunctionCandidate.cpp | 3 +-
src/c++/lib/manta/SVMultiJunctionCandidate.hh | 3 +-
src/c++/lib/manta/SVMultiJunctionCandidateUtil.hh | 3 +-
src/c++/lib/manta/SVReferenceUtil.cpp | 3 +-
src/c++/lib/manta/SVReferenceUtil.hh | 3 +-
src/c++/lib/manta/SVScoreInfo.cpp | 3 +-
src/c++/lib/manta/SVScoreInfo.hh | 3 +-
src/c++/lib/manta/SVScoreInfoDiploid.cpp | 9 +-
src/c++/lib/manta/SVScoreInfoDiploid.hh | 10 +-
src/c++/lib/manta/SVScoreInfoSomatic.cpp | 3 +-
src/c++/lib/manta/SVScoreInfoSomatic.hh | 3 +-
src/c++/lib/manta/SVScoreInfoTumor.hh | 3 +-
src/c++/lib/manta/ShadowReadFinder.cpp | 3 +-
src/c++/lib/manta/ShadowReadFinder.hh | 3 +-
src/c++/lib/manta/test/CMakeLists.txt | 2 +-
.../manta/test/SVLocusScannerSemiAlignedTest.cpp | 3 +-
src/c++/lib/manta/test/SVLocusScannerTest.cpp | 7 +-
src/c++/lib/manta/test/test_main.cpp | 3 +-
src/c++/lib/options/AlignmentFileOptions.hh | 3 +-
src/c++/lib/options/AlignmentFileOptionsParser.cpp | 3 +-
src/c++/lib/options/AlignmentFileOptionsParser.hh | 3 +-
src/c++/lib/options/CMakeLists.txt | 2 +-
src/c++/lib/options/CallOptionsDiploid.cpp | 3 +-
src/c++/lib/options/CallOptionsDiploid.hh | 3 +-
src/c++/lib/options/CallOptionsShared.hh | 3 +-
src/c++/lib/options/CallOptionsSomatic.cpp | 3 +-
src/c++/lib/options/CallOptionsSomatic.hh | 3 +-
src/c++/lib/options/CallOptionsTumor.cpp | 3 +-
src/c++/lib/options/CallOptionsTumor.hh | 3 +-
src/c++/lib/options/IterativeAssemblerOptions.hh | 3 +-
src/c++/lib/options/ReadScannerOptions.hh | 3 +-
src/c++/lib/options/ReadScannerOptionsParser.cpp | 3 +-
src/c++/lib/options/ReadScannerOptionsParser.hh | 3 +-
src/c++/lib/options/SVLocusSetOptions.hh | 3 +-
src/c++/lib/options/SVLocusSetOptionsParser.cpp | 3 +-
src/c++/lib/options/SVLocusSetOptionsParser.hh | 3 +-
src/c++/lib/options/SVRefinerOptions.hh | 3 +-
src/c++/lib/options/SmallAssemblerOptions.hh | 3 +-
src/c++/lib/options/optionsUtil.cpp | 3 +-
src/c++/lib/options/optionsUtil.hh | 3 +-
src/c++/lib/svgraph/CMakeLists.txt | 2 +-
src/c++/lib/svgraph/EdgeInfo.cpp | 3 +-
src/c++/lib/svgraph/EdgeInfo.hh | 3 +-
src/c++/lib/svgraph/EdgeInfoUtil.cpp | 3 +-
src/c++/lib/svgraph/EdgeInfoUtil.hh | 3 +-
src/c++/lib/svgraph/GenomeInterval.cpp | 3 +-
src/c++/lib/svgraph/GenomeInterval.hh | 3 +-
src/c++/lib/svgraph/GenomeIntervalTracker.hh | 3 +-
src/c++/lib/svgraph/GenomeIntervalUtil.cpp | 3 +-
src/c++/lib/svgraph/GenomeIntervalUtil.hh | 3 +-
src/c++/lib/svgraph/SVLocus.cpp | 3 +-
src/c++/lib/svgraph/SVLocus.hh | 32 +-
src/c++/lib/svgraph/SVLocusNode.cpp | 3 +-
src/c++/lib/svgraph/SVLocusNode.hh | 83 +++--
src/c++/lib/svgraph/SVLocusSampleCounts.cpp | 3 +-
src/c++/lib/svgraph/SVLocusSampleCounts.hh | 3 +-
src/c++/lib/svgraph/SVLocusSet.cpp | 3 +-
src/c++/lib/svgraph/SVLocusSet.hh | 50 ++-
src/c++/lib/svgraph/test/CMakeLists.txt | 2 +-
src/c++/lib/svgraph/test/GenomeIntervalTest.cpp | 3 +-
.../lib/svgraph/test/GenomeIntervalUtilTest.cpp | 3 +-
src/c++/lib/svgraph/test/SVLocusNodeTest.cpp | 3 +-
src/c++/lib/svgraph/test/SVLocusSerializeTest.cpp | 3 +-
src/c++/lib/svgraph/test/SVLocusSetPrivateTest.cpp | 3 +-
.../lib/svgraph/test/SVLocusSetSerializeTest.cpp | 3 +-
src/c++/lib/svgraph/test/SVLocusSetTest.cpp | 3 +-
src/c++/lib/svgraph/test/SVLocusTest.cpp | 3 +-
src/c++/lib/svgraph/test/SVLocusTestUtil.hh | 3 +-
src/c++/lib/svgraph/test/test_main.cpp | 3 +-
src/cmake/boost.cmake | 2 +-
src/cmake/bootstrap/common.bash | 2 +-
src/cmake/bootstrap/installCmake.bash | 2 +-
src/cmake/buildTimeConfigure.cmake | 2 +-
src/cmake/cxxCommon.cmake | 2 +-
src/cmake/cxxConfigure.cmake | 51 ++-
src/cmake/cxxExecutable.cmake | 2 +-
src/cmake/cxxLibrary.cmake | 2 +-
src/cmake/cxxTestLibrary.cmake | 2 +-
src/cmake/getBuildTimeConfigInfo.cmake | 2 +-
src/cmake/globals.cmake | 2 +-
src/cmake/macros.cmake | 2 +-
src/cmake/postInstall/CMakeLists.txt | 2 +-
src/cmake/preInstall/CMakeLists.txt | 2 +-
.../checkTargetPathsWritable/CMakeLists.txt | 2 +-
.../checkTargetPathWritable.cmake | 2 +-
.../preInstall/copyrightAndChanges/CMakeLists.txt | 2 +-
src/demo/CMakeLists.txt | 2 +-
src/demo/data/CMakeLists.txt | 2 +-
src/demo/runMantaWorkflowDemo.py | 2 +-
src/python/CMakeLists.txt | 2 +-
src/python/bin/CMakeLists.txt | 2 +-
src/python/bin/configManta.py | 7 +-
src/python/lib/CMakeLists.txt | 2 +-
src/python/lib/checkChromSet.py | 4 +-
src/python/lib/configBuildTimeInfo.py | 2 +-
src/python/lib/configureOptions.py | 17 +-
src/python/lib/configureUtil.py | 20 +-
src/python/lib/estimateHardware.py | 2 +-
src/python/lib/makeRunScript.py | 2 +-
src/python/lib/mantaOptions.py | 2 +-
src/python/lib/mantaWorkflow.py | 28 +-
src/python/lib/sharedWorkflow.py | 3 +-
src/python/lib/workflowUtil.py | 42 ++-
src/python/libexec/CMakeLists.txt | 2 +-
src/python/libexec/cat.py | 2 +-
src/python/libexec/denovo_scoring.py | 2 +-
src/python/libexec/extractSmallIndelCandidates.py | 2 +-
src/python/libexec/filterBam.py | 2 +-
src/python/libexec/mergeBam.py | 2 +-
src/python/libexec/mergeChromDepth.py | 4 +-
src/python/libexec/ploidyFilter.py | 2 +-
src/python/libexec/sortBam.py | 2 +-
src/python/libexec/sortEdgeLogs.py | 2 +-
src/python/libexec/sortVcf.py | 10 +-
src/python/libexec/vcfCmdlineSwapper.py | 2 +-
src/srcqc/check_for_nonascii_source.bash | 2 +-
src/srcqc/run_cppcheck.py | 2 +-
536 files changed, 2075 insertions(+), 1471 deletions(-)
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