[med-svn] [freebayes] branch upstream updated (55cd62b -> 28bfd02)
Andreas Tille
tille at debian.org
Wed May 28 17:27:42 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository freebayes.
from 55cd62b Imported Upstream version 0.9.10.11
new 28bfd02 Imported Upstream version 0.9.14+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:
.gitmodules | 6 +-
Makefile | 8 +-
README.md | 2 +-
bamtools/CMakeLists.txt | 65 -
bamtools/LICENSE | 22 -
bamtools/README | 60 -
bamtools/docs/Doxyfile | 1605 --
bamtools/src/CMakeLists.txt | 16 -
bamtools/src/ExportHeader.cmake | 27 -
bamtools/src/api/BamAlgorithms.h | 21 -
bamtools/src/api/BamAlignment.cpp | 1083 -
bamtools/src/api/BamAlignment.h | 638 -
bamtools/src/api/BamAux.h | 468 -
bamtools/src/api/BamConstants.h | 282 -
bamtools/src/api/BamIndex.h | 90 -
bamtools/src/api/BamMultiReader.cpp | 421 -
bamtools/src/api/BamMultiReader.h | 127 -
bamtools/src/api/BamReader.cpp | 383 -
bamtools/src/api/BamReader.h | 119 -
bamtools/src/api/BamWriter.cpp | 152 -
bamtools/src/api/BamWriter.h | 69 -
bamtools/src/api/CMakeLists.txt | 83 -
bamtools/src/api/IBamIODevice.h | 98 -
bamtools/src/api/SamConstants.h | 97 -
bamtools/src/api/SamHeader.cpp | 236 -
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bamtools/src/api/SamProgram.cpp | 139 -
bamtools/src/api/SamProgram.h | 61 -
bamtools/src/api/SamProgramChain.cpp | 354 -
bamtools/src/api/SamProgramChain.h | 85 -
bamtools/src/api/SamReadGroup.cpp | 221 -
bamtools/src/api/SamReadGroup.h | 68 -
bamtools/src/api/SamReadGroupDictionary.cpp | 297 -
bamtools/src/api/SamReadGroupDictionary.h | 85 -
bamtools/src/api/SamSequence.cpp | 161 -
bamtools/src/api/SamSequence.h | 60 -
bamtools/src/api/SamSequenceDictionary.cpp | 301 -
bamtools/src/api/SamSequenceDictionary.h | 86 -
bamtools/src/api/algorithms/Sort.h | 335 -
bamtools/src/api/api_global.h | 21 -
bamtools/src/api/internal/CMakeLists.txt | 25 -
bamtools/src/api/internal/bam/BamHeader_p.cpp | 125 -
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bamtools/src/api/internal/io/RollingBuffer_p.cpp | 314 -
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bamtools/src/third_party/gtest-1.6.0/src/gtest.cc | 4898 -----
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bamtools/src/third_party/jsoncpp/CMakeLists.txt | 23 -
bamtools/src/third_party/jsoncpp/LICENSE | 55 -
bamtools/src/third_party/jsoncpp/json.h | 15 -
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bamtools/src/third_party/jsoncpp/json_config.h | 42 -
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bamtools/src/third_party/jsoncpp/json_reader.cpp | 870 -
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bamtools/src/third_party/jsoncpp/json_tool.h | 93 -
bamtools/src/third_party/jsoncpp/json_value.cpp | 1701 --
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bamtools/src/third_party/jsoncpp/json_writer.cpp | 819 -
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bamtools/src/toolkit/CMakeLists.txt | 44 -
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bamtools/src/utils/bamtools_filter_engine.h | 552 -
bamtools/src/utils/bamtools_filter_properties.h | 195 -
bamtools/src/utils/bamtools_filter_ruleparser.h | 319 -
bamtools/src/utils/bamtools_options.cpp | 287 -
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bamtools/src/utils/bamtools_pileup_engine.cpp | 346 -
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bamtools/src/utils/bamtools_utilities.cpp | 333 -
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bamtools/src/utils/bamtools_variant.h | 128 -
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intervaltree/interval_tree_test.cpp | 81 -
src/Allele.cpp | 3 +-
src/AlleleParser.cpp | 3 +
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delete mode 100644 vcflib/tabixpp/perl/t/02remote.t
delete mode 100644 vcflib/tabixpp/perl/typemap
delete mode 100644 vcflib/tabixpp/python/setup.py
delete mode 100644 vcflib/tabixpp/python/tabixmodule.c
delete mode 100755 vcflib/tabixpp/python/test.py
delete mode 100644 vcflib/tabixpp/tabix.1
delete mode 100644 vcflib/tabixpp/tabix.cpp
delete mode 100644 vcflib/tabixpp/tabix.h
delete mode 100644 vcflib/tabixpp/tabix.hpp
delete mode 100755 vcflib/tabixpp/tabix.py
delete mode 100644 vcflib/tabixpp/tabix.tex
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