[med-svn] [jellyfish] 03/05: Merge tag 'upstream/2.1.4'
Andreas Tille
tille at debian.org
Sat Oct 4 17:38:58 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository jellyfish.
commit deb4093318f9f16a3d4c44a7f44b9fabeebdf3e8
Merge: 2f32ad8 91d6a38
Author: Andreas Tille <tille at debian.org>
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(-)
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