This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch libjsoncpp in repository jellyfish1.
commit deb4093318f9f16a3d4c44a7f44b9fabeebdf3e8 Merge: 2f32ad8 91d6a38 Author: Andreas Tille <[email protected]> Date: Sat Oct 4 19:09:06 2014 +0200 Merge tag 'upstream/2.1.4' Upstream version 2.1.4 Conflicts: .gitignore .gitignore | 16 +- CHANGES | 13 + Makefile.am | 327 +- Makefile.in | 1826 -- Makefile.simple | 40 + README | 22 +- README.md | 32 + aclocal.m4 | 1033 - config.guess | 1530 -- config.h.in | 90 - config.sub | 1773 -- configure | 18209 ----------------- configure.ac | 64 +- depcomp | 708 - development.mk | 22 + doc/Makefile | 37 + doc/UserGuide.lyx | 1515 ++ doc/generate_options_tex.sh | 7 + doc/help_parse.rb | 451 + doc/help_parse.treetop | 52 + doc/jellyfish.html | 802 + doc/jellyfish.tex | 205 + doc/option_to_tex | 35 + doc/options.tex | 210 + doc/transfile | 19 + examples/README | 15 + examples/count_in_file/Makefile | 7 + examples/count_in_file/README | 40 + examples/count_in_file/count_in_file.cc | 158 + examples/query_per_sequence/Makefile | 10 + examples/query_per_sequence/README | 18 + examples/query_per_sequence/query_per_sequence.cc | 86 + examples/query_per_sequence/sequence_mers.hpp | 99 + gtest.mk | 49 +- .../reversible_hash_function.hpp => header-license | 7 - include/jellyfish/allocators_mmap.hpp | 78 + include/jellyfish/atomic_bits_array.hpp | 202 + include/jellyfish/atomic_field.hpp | 157 + {jellyfish => include/jellyfish}/atomic_gcc.hpp | 2 +- {jellyfish => include/jellyfish}/backtrace.hpp | 0 include/jellyfish/binary_dumper.hpp | 224 + include/jellyfish/bloom_common.hpp | 129 + include/jellyfish/bloom_counter2.hpp | 221 + include/jellyfish/bloom_filter.hpp | 164 + include/jellyfish/circular_buffer.hpp | 200 + include/jellyfish/compare_and_swap.hpp | 80 + include/jellyfish/cooperative_pool.hpp | 258 + include/jellyfish/cooperative_pool2.hpp | 283 + include/jellyfish/cpp_array.hpp | 156 + include/jellyfish/divisor.hpp | 150 + include/jellyfish/dumper.hpp | 103 + include/jellyfish/err.hpp | 99 + include/jellyfish/file_header.hpp | 112 + include/jellyfish/generator_manager.hpp | 163 + include/jellyfish/generic_file_header.hpp | 255 + include/jellyfish/hash_counter.hpp | 244 + include/jellyfish/int128.hpp | 203 + include/jellyfish/jellyfish.hpp | 37 + include/jellyfish/json.h | 1855 ++ include/jellyfish/large_hash_array.hpp | 994 + include/jellyfish/large_hash_iterator.hpp | 260 + include/jellyfish/locks_pthread.hpp | 211 + include/jellyfish/mapped_file.hpp | 220 + include/jellyfish/mer_dna.hpp | 729 + include/jellyfish/mer_dna_bloom_counter.hpp | 50 + include/jellyfish/mer_heap.hpp | 115 + include/jellyfish/mer_iterator.hpp | 100 + include/jellyfish/mer_overlap_sequence_parser.hpp | 241 + include/jellyfish/mer_qual_iterator.hpp | 118 + include/jellyfish/misc.hpp | 247 + include/jellyfish/offsets_key_value.hpp | 277 + include/jellyfish/rectangular_binary_matrix.hpp | 379 + .../jellyfish}/simple_circular_buffer.hpp | 14 +- include/jellyfish/sorted_dumper.hpp | 115 + include/jellyfish/stdio_filebuf.hpp | 170 + {jellyfish => include/jellyfish}/storage.hpp | 4 +- include/jellyfish/stream_iterator.hpp | 90 + include/jellyfish/stream_manager.hpp | 157 + include/jellyfish/text_dumper.hpp | 88 + {jellyfish => include/jellyfish}/thread_exec.hpp | 2 + {jellyfish => include/jellyfish}/time.hpp | 0 {jellyfish => include/jellyfish}/token_ring.hpp | 80 +- include/jellyfish/whole_sequence_parser.hpp | 150 + install-sh | 527 - jellyfish-1.1.pc.in => jellyfish-2.0.pc.in | 2 +- jellyfish/aligned_values_array.hpp | 141 - jellyfish/allocators_malloc.hpp | 61 - jellyfish/allocators_mmap.hpp | 64 - jellyfish/allocators_shm.hpp | 94 - jellyfish/capped_integer.hpp | 64 - jellyfish/circular_buffer.hpp | 68 - jellyfish/cite_cmdline.hpp | 111 - jellyfish/compacted_dumper.hpp | 171 - jellyfish/compacted_hash.hpp | 530 - jellyfish/concurrent_queues.hpp | 160 - jellyfish/count_main_cmdline.hpp | 684 - jellyfish/counter.hpp | 52 - jellyfish/dbg.cc | 7 - jellyfish/direct_indexing_array.hpp | 151 - jellyfish/direct_sorted_dumper.hpp | 131 - jellyfish/divisor.hpp | 135 - jellyfish/dna_codes.cc | 28 - jellyfish/dna_codes.hpp | 20 - jellyfish/double_fifo_input.hpp | 192 - jellyfish/dump_fastq_main.cc | 71 - jellyfish/dump_fastq_main_cmdline.hpp | 160 - jellyfish/dump_main.cc | 100 - jellyfish/dump_main_cmdline.hpp | 151 - jellyfish/dumper.hpp | 61 - jellyfish/eLut.h | 71 - jellyfish/err.hpp | 145 - jellyfish/fastq_dumper.hpp | 131 - jellyfish/file_parser.cc | 99 - jellyfish/file_parser.hpp | 92 - jellyfish/floats.cc | 23 - jellyfish/floats.hpp | 71 - jellyfish/generate_sequence.cc | 199 +- jellyfish/generate_sequence_cmdline.hpp | 171 - jellyfish/generate_sequence_cmdline.yaggo | 27 + jellyfish/half.cpp | 311 - jellyfish/half.h | 766 - jellyfish/hash.hpp | 253 - jellyfish/hash_fastq_merge.cc | 52 - jellyfish/hash_fastq_merge_cmdline.hpp | 171 - jellyfish/hash_merge.cc | 242 - jellyfish/hash_merge_cmdline.hpp | 157 - jellyfish/heap.hpp | 125 - jellyfish/histo_fastq_main.cc | 70 - jellyfish/histo_fastq_main_cmdline.hpp | 142 - jellyfish/histo_main.cc | 132 - jellyfish/histo_main_cmdline.hpp | 199 - jellyfish/invertible_hash_array.hpp | 1015 - jellyfish/locking_hash_counters.hpp | 372 - jellyfish/locks_pthread.hpp | 172 - jellyfish/mapped_file.cc | 25 - jellyfish/mapped_file.hpp | 181 - jellyfish/mer_counter.cc | 379 - jellyfish/mer_counting.hpp | 68 - jellyfish/merge_files.cc | 151 + jellyfish/{err.cc => merge_files.hpp} | 23 +- jellyfish/misc.hpp | 144 - jellyfish/noop_dumper.hpp | 30 - jellyfish/offsets_key_value.hpp | 239 - jellyfish/parse_dna.cc | 59 - jellyfish/parse_dna.hpp | 194 - jellyfish/parse_quake.cc | 107 - jellyfish/parse_quake.hpp | 152 - jellyfish/parse_qual_dna.cc | 74 - jellyfish/parse_qual_dna.hpp | 147 - jellyfish/parse_read.hpp | 105 - jellyfish/query_cmdline.hpp | 135 - jellyfish/query_main.cc | 76 - jellyfish/randomc.h | 4 +- jellyfish/raw_dumper.hpp | 244 - jellyfish/read_parser.cc | 108 - jellyfish/read_parser.hpp | 78 - jellyfish/seq_qual_parser.cc | 139 - jellyfish/seq_qual_parser.hpp | 66 - jellyfish/sequence_parser.cc | 104 - jellyfish/sequence_parser.hpp | 71 - jellyfish/simple_growing_array.hpp | 60 - jellyfish/sorted_dumper.hpp | 166 - jellyfish/square_binary_matrix.cc | 289 - jellyfish/square_binary_matrix.hpp | 203 - jellyfish/stats_main.cc | 121 - jellyfish/stats_main_cmdline.hpp | 160 - jellyfish/storage.cc | 51 - jellyfish/test_double_fifo_input.cc | 79 - jellyfish/test_read_parser.cc | 50 - jellyfish/toFloat.h | 16391 --------------- jellyfish/yaggo.cpp | 184 - jellyfish/yaggo.hpp | 152 - {jellyfish => lib}/allocators_mmap.cc | 76 +- {jellyfish => lib}/err.cc | 6 +- lib/generator_manager.cc | 281 + lib/int128.cc | 94 + lib/jsoncpp.cpp | 4230 ++++ jellyfish/hash_function.hpp => lib/mer_dna.cc | 10 +- {jellyfish => lib}/misc.cc | 40 + lib/rectangular_binary_matrix.cc | 216 + lib/storage.cc | 51 + {jellyfish => lib}/thread_exec.cc | 12 +- {jellyfish => lib}/time.cc | 0 local.mk | 3 + ltmain.sh | 9655 --------- m4/.gitignore | 4 + m4/libtool.m4 | 7986 -------- m4/ltoptions.m4 | 384 - m4/ltsugar.m4 | 123 - m4/ltversion.m4 | 23 - m4/lt~obsolete.m4 | 98 - missing | 331 - sub_commands/bc_main.cc | 161 + sub_commands/bc_main_cmdline.yaggo | 45 + jellyfish/cite.cc => sub_commands/cite_main.cc | 11 +- sub_commands/cite_main_cmdline.yaggo | 12 + sub_commands/count_main.cc | 354 + sub_commands/count_main_cmdline.yaggo | 102 + sub_commands/dump_main.cc | 88 + sub_commands/dump_main_cmdline.yaggo | 24 + sub_commands/histo_main.cc | 90 + sub_commands/histo_main_cmdline.yaggo | 38 + sub_commands/info_main.cc | 54 + sub_commands/info_main_cmdline.yaggo | 23 + {jellyfish => sub_commands}/jellyfish.cc | 18 +- sub_commands/mem_main.cc | 54 + sub_commands/mem_main_cmdline.yaggo | 123 + .../parse_read.cc => sub_commands/merge_main.cc | 45 +- sub_commands/merge_main_cmdline.yaggo | 15 + sub_commands/query_main.cc | 123 + sub_commands/query_main_cmdline.yaggo | 24 + sub_commands/stats_main.cc | 83 + sub_commands/stats_main_cmdline.yaggo | 28 + swig/Readme.md | 154 + swig/Tuprules.tup | 120 + swig/hash_counter.i | 56 + swig/hash_set.i | 35 + swig/jellyfish.i | 28 + swig/mer_dna.i | 99 + swig/mer_file.i | 191 + swig/perl5/Makefile.PL | 20 + swig/perl5/Tupfile | 14 + swig/perl5/t/test_hash_counter.t | 44 + swig/perl5/t/test_mer_file.t | 51 + swig/python/Tupfile | 14 + swig/python/setup.py | 45 + swig/python/test_hash_counter.py | 39 + swig/python/test_mer_file.py | 57 + swig/ruby/Tupfile | 14 + swig/ruby/extconf.rb | 12 + swig/ruby/test_hash_counter.rb | 42 + swig/ruby/test_mer_file.rb | 57 + swig/tests/Tupfile | 6 + tests/big.sh | 15 +- tests/bloom_counter.sh | 47 + tests/bloom_filter.sh | 23 + tests/compat.sh.in | 7 +- tests/from_stream.sh | 2 +- tests/from_stream_fastq.sh | 2 +- tests/generate_sequence.sh | 6 + tests/large_key.sh | 18 + tests/merge.sh | 36 +- tests/min_qual.sh | 2 +- tests/multi_file.sh | 48 +- tests/multi_file_fastq.sh | 2 +- tests/parallel_direct_indexing.sh | 2 +- tests/parallel_fastq_direct_indexing.sh | 2 +- tests/parallel_fastq_hashing.sh | 2 +- tests/parallel_fastq_sequence_hashing.sh | 2 +- tests/parallel_hashing.sh | 99 +- tests/parsers.sh | 2 +- tests/quality_filter.sh | 25 + tests/raw_hash.sh | 2 +- tests/serial_direct_indexing.sh | 2 +- tests/serial_hashing.sh | 2 +- tests/small.sh | 2 +- tests/subset_hashing.sh | 19 + unit_tests/Makefile | 82 + unit_tests/gtest/gtest.h | 20061 +++++++++++++++++++ unit_tests/gtest/include/gtest/gtest-death-test.h | 283 - unit_tests/gtest/include/gtest/gtest-message.h | 230 - unit_tests/gtest/include/gtest/gtest-param-test.h | 1421 -- unit_tests/gtest/include/gtest/gtest-printers.h | 796 - unit_tests/gtest/include/gtest/gtest-spi.h | 232 - unit_tests/gtest/include/gtest/gtest-test-part.h | 176 - unit_tests/gtest/include/gtest/gtest-typed-test.h | 259 - unit_tests/gtest/include/gtest/gtest.h | 2155 -- unit_tests/gtest/include/gtest/gtest_pred_impl.h | 358 - unit_tests/gtest/include/gtest/gtest_prod.h | 58 - .../gtest/internal/gtest-death-test-internal.h | 308 - .../gtest/include/gtest/internal/gtest-filepath.h | 210 - .../gtest/include/gtest/internal/gtest-internal.h | 1236 -- .../include/gtest/internal/gtest-linked_ptr.h | 233 - .../gtest/internal/gtest-param-util-generated.h | 4822 ----- .../include/gtest/internal/gtest-param-util.h | 619 - .../gtest/include/gtest/internal/gtest-port.h | 1785 -- .../gtest/include/gtest/internal/gtest-string.h | 360 - .../gtest/include/gtest/internal/gtest-tuple.h | 968 - .../gtest/include/gtest/internal/gtest-type-util.h | 3330 --- unit_tests/gtest/src/gtest-all.cc | 9558 ++++++++- unit_tests/gtest/src/gtest-death-test.cc | 1234 -- unit_tests/gtest/src/gtest-filepath.cc | 380 - unit_tests/gtest/src/gtest-internal-inl.h | 1038 - unit_tests/gtest/src/gtest-port.cc | 752 - unit_tests/gtest/src/gtest-printers.cc | 356 - unit_tests/gtest/src/gtest-test-part.cc | 110 - unit_tests/gtest/src/gtest-typed-test.cc | 110 - unit_tests/gtest/src/gtest.cc | 4898 ----- unit_tests/gtest/src/gtest_main.cc | 5 +- unit_tests/test_allocators_mmap.cc | 15 + unit_tests/test_atomic_bits_array.cc | 32 + unit_tests/test_cond.cc | 80 + unit_tests/test_cooperative_pool2.cc | 89 + unit_tests/test_dumpers.cc | 144 + unit_tests/test_file_header.cc | 90 + unit_tests/test_generator_manager.cc | 95 + unit_tests/test_hash_counter.cc | 104 + unit_tests/test_int128.cc | 34 + unit_tests/test_large_block.cc | 33 + unit_tests/test_large_hash_array.cc | 346 + unit_tests/test_main.cc | 67 + unit_tests/test_main.hpp | 26 + unit_tests/test_main_cmdline.yaggo | 10 + unit_tests/test_mapped_file.cc | 54 + unit_tests/test_mer_dna.cc | 529 + unit_tests/test_mer_dna_bloom_counter.cc | 150 + unit_tests/test_mer_heap.cc | 76 + unit_tests/test_mer_iterator.cc | 181 + unit_tests/test_mer_overlap_sequence_parser.cc | 177 + unit_tests/test_misc.cc | 110 + unit_tests/test_mutex.cc | 53 + unit_tests/test_offsets_key_value.cc | 299 +- unit_tests/test_packed_key_value_array.cc | 213 + unit_tests/test_rectangular_binary_matrix.cc | 332 + unit_tests/test_simple_circular_buffer.cc | 105 +- unit_tests/test_square_binary_matrix.cc | 10 +- unit_tests/test_stdio_filebuf.cc | 55 + unit_tests/test_stream_iterator.cc | 94 + unit_tests/test_text_dumper.cc | 115 + unit_tests/test_token_ring.cc | 44 + unit_tests/test_whole_sequence_parser.cc | 161 + unit_tests/unit_tests.sh | 6 +- 322 files changed, 55831 insertions(+), 102992 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/jellyfish1.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
