[med-svn] [jellyfish] branch upstream updated (e7fb264 -> 91d6a38)
Andreas Tille
tille at debian.org
Sat Oct 4 17:38:59 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository jellyfish.
from e7fb264 Imported Upstream version 1.1.11
new 91d6a38 Imported Upstream version 2.1.4
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:
.gitignore | 15 +
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.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.cc | 40 -
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 +
jellyfish/floats.cc => sub_commands/merge_main.cc | 26 +-
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, 55830 insertions(+), 102990 deletions(-)
create mode 100644 .gitignore
create mode 100644 CHANGES
delete mode 100644 Makefile.in
create mode 100644 Makefile.simple
create mode 100644 README.md
delete mode 100644 aclocal.m4
delete mode 100755 config.guess
delete mode 100644 config.h.in
delete mode 100755 config.sub
delete mode 100755 configure
delete mode 100755 depcomp
create mode 100644 development.mk
create mode 100644 doc/Makefile
create mode 100644 doc/UserGuide.lyx
create mode 100755 doc/generate_options_tex.sh
create mode 100644 doc/help_parse.rb
create mode 100644 doc/help_parse.treetop
create mode 100644 doc/jellyfish.html
create mode 100644 doc/jellyfish.tex
create mode 100644 doc/option_to_tex
create mode 100644 doc/options.tex
create mode 100644 doc/transfile
create mode 100644 examples/README
create mode 100644 examples/count_in_file/Makefile
create mode 100644 examples/count_in_file/README
create mode 100644 examples/count_in_file/count_in_file.cc
create mode 100644 examples/query_per_sequence/Makefile
create mode 100644 examples/query_per_sequence/README
create mode 100644 examples/query_per_sequence/query_per_sequence.cc
create mode 100644 examples/query_per_sequence/sequence_mers.hpp
rename jellyfish/reversible_hash_function.hpp => header-license (82%)
create mode 100644 include/jellyfish/allocators_mmap.hpp
create mode 100644 include/jellyfish/atomic_bits_array.hpp
create mode 100644 include/jellyfish/atomic_field.hpp
rename {jellyfish => include/jellyfish}/atomic_gcc.hpp (97%)
rename {jellyfish => include/jellyfish}/backtrace.hpp (100%)
create mode 100644 include/jellyfish/binary_dumper.hpp
create mode 100644 include/jellyfish/bloom_common.hpp
create mode 100644 include/jellyfish/bloom_counter2.hpp
create mode 100644 include/jellyfish/bloom_filter.hpp
create mode 100644 include/jellyfish/circular_buffer.hpp
create mode 100644 include/jellyfish/compare_and_swap.hpp
create mode 100644 include/jellyfish/cooperative_pool.hpp
create mode 100644 include/jellyfish/cooperative_pool2.hpp
create mode 100644 include/jellyfish/cpp_array.hpp
create mode 100644 include/jellyfish/divisor.hpp
create mode 100644 include/jellyfish/dumper.hpp
create mode 100644 include/jellyfish/err.hpp
create mode 100644 include/jellyfish/file_header.hpp
create mode 100644 include/jellyfish/generator_manager.hpp
create mode 100644 include/jellyfish/generic_file_header.hpp
create mode 100644 include/jellyfish/hash_counter.hpp
create mode 100644 include/jellyfish/int128.hpp
create mode 100644 include/jellyfish/jellyfish.hpp
create mode 100644 include/jellyfish/json.h
create mode 100644 include/jellyfish/large_hash_array.hpp
create mode 100644 include/jellyfish/large_hash_iterator.hpp
create mode 100644 include/jellyfish/locks_pthread.hpp
create mode 100644 include/jellyfish/mapped_file.hpp
create mode 100644 include/jellyfish/mer_dna.hpp
create mode 100644 include/jellyfish/mer_dna_bloom_counter.hpp
create mode 100644 include/jellyfish/mer_heap.hpp
create mode 100644 include/jellyfish/mer_iterator.hpp
create mode 100644 include/jellyfish/mer_overlap_sequence_parser.hpp
create mode 100644 include/jellyfish/mer_qual_iterator.hpp
create mode 100644 include/jellyfish/misc.hpp
create mode 100644 include/jellyfish/offsets_key_value.hpp
create mode 100644 include/jellyfish/rectangular_binary_matrix.hpp
rename {jellyfish => include/jellyfish}/simple_circular_buffer.hpp (98%)
create mode 100644 include/jellyfish/sorted_dumper.hpp
create mode 100644 include/jellyfish/stdio_filebuf.hpp
rename {jellyfish => include/jellyfish}/storage.hpp (95%)
create mode 100644 include/jellyfish/stream_iterator.hpp
create mode 100644 include/jellyfish/stream_manager.hpp
create mode 100644 include/jellyfish/text_dumper.hpp
rename {jellyfish => include/jellyfish}/thread_exec.hpp (96%)
rename {jellyfish => include/jellyfish}/time.hpp (100%)
rename {jellyfish => include/jellyfish}/token_ring.hpp (57%)
create mode 100644 include/jellyfish/whole_sequence_parser.hpp
delete mode 100755 install-sh
rename jellyfish-1.1.pc.in => jellyfish-2.0.pc.in (84%)
delete mode 100644 jellyfish/aligned_values_array.hpp
delete mode 100644 jellyfish/allocators_malloc.hpp
delete mode 100644 jellyfish/allocators_mmap.hpp
delete mode 100644 jellyfish/allocators_shm.hpp
delete mode 100644 jellyfish/capped_integer.hpp
delete mode 100644 jellyfish/circular_buffer.hpp
delete mode 100644 jellyfish/cite_cmdline.hpp
delete mode 100644 jellyfish/compacted_dumper.hpp
delete mode 100644 jellyfish/compacted_hash.hpp
delete mode 100644 jellyfish/concurrent_queues.hpp
delete mode 100644 jellyfish/count_main_cmdline.hpp
delete mode 100644 jellyfish/counter.hpp
delete mode 100644 jellyfish/direct_indexing_array.hpp
delete mode 100644 jellyfish/direct_sorted_dumper.hpp
delete mode 100644 jellyfish/divisor.hpp
delete mode 100644 jellyfish/dna_codes.cc
delete mode 100644 jellyfish/dna_codes.hpp
delete mode 100644 jellyfish/double_fifo_input.hpp
delete mode 100644 jellyfish/dump_fastq_main.cc
delete mode 100644 jellyfish/dump_fastq_main_cmdline.hpp
delete mode 100644 jellyfish/dump_main.cc
delete mode 100644 jellyfish/dump_main_cmdline.hpp
delete mode 100644 jellyfish/dumper.hpp
delete mode 100644 jellyfish/eLut.h
delete mode 100644 jellyfish/err.hpp
delete mode 100644 jellyfish/fastq_dumper.hpp
delete mode 100644 jellyfish/file_parser.cc
delete mode 100644 jellyfish/file_parser.hpp
delete mode 100644 jellyfish/floats.hpp
delete mode 100644 jellyfish/generate_sequence_cmdline.hpp
create mode 100644 jellyfish/generate_sequence_cmdline.yaggo
delete mode 100644 jellyfish/half.cpp
delete mode 100644 jellyfish/half.h
delete mode 100644 jellyfish/hash.hpp
delete mode 100644 jellyfish/hash_fastq_merge.cc
delete mode 100644 jellyfish/hash_fastq_merge_cmdline.hpp
delete mode 100644 jellyfish/hash_merge.cc
delete mode 100644 jellyfish/hash_merge_cmdline.hpp
delete mode 100644 jellyfish/heap.hpp
delete mode 100644 jellyfish/histo_fastq_main.cc
delete mode 100644 jellyfish/histo_fastq_main_cmdline.hpp
delete mode 100644 jellyfish/histo_main.cc
delete mode 100644 jellyfish/histo_main_cmdline.hpp
delete mode 100644 jellyfish/invertible_hash_array.hpp
delete mode 100644 jellyfish/locking_hash_counters.hpp
delete mode 100644 jellyfish/locks_pthread.hpp
delete mode 100644 jellyfish/mapped_file.cc
delete mode 100644 jellyfish/mapped_file.hpp
delete mode 100644 jellyfish/mer_counter.cc
delete mode 100644 jellyfish/mer_counting.hpp
create mode 100644 jellyfish/merge_files.cc
copy jellyfish/{err.cc => merge_files.hpp} (63%)
delete mode 100644 jellyfish/misc.hpp
delete mode 100644 jellyfish/noop_dumper.hpp
delete mode 100644 jellyfish/offsets_key_value.hpp
delete mode 100644 jellyfish/parse_dna.cc
delete mode 100644 jellyfish/parse_dna.hpp
delete mode 100644 jellyfish/parse_quake.cc
delete mode 100644 jellyfish/parse_quake.hpp
delete mode 100644 jellyfish/parse_qual_dna.cc
delete mode 100644 jellyfish/parse_qual_dna.hpp
delete mode 100644 jellyfish/parse_read.cc
delete mode 100644 jellyfish/parse_read.hpp
delete mode 100644 jellyfish/query_cmdline.hpp
delete mode 100644 jellyfish/query_main.cc
delete mode 100644 jellyfish/raw_dumper.hpp
delete mode 100644 jellyfish/read_parser.cc
delete mode 100644 jellyfish/read_parser.hpp
delete mode 100644 jellyfish/seq_qual_parser.cc
delete mode 100644 jellyfish/seq_qual_parser.hpp
delete mode 100644 jellyfish/sequence_parser.cc
delete mode 100644 jellyfish/sequence_parser.hpp
delete mode 100644 jellyfish/simple_growing_array.hpp
delete mode 100644 jellyfish/sorted_dumper.hpp
delete mode 100644 jellyfish/square_binary_matrix.cc
delete mode 100644 jellyfish/square_binary_matrix.hpp
delete mode 100644 jellyfish/stats_main.cc
delete mode 100644 jellyfish/stats_main_cmdline.hpp
delete mode 100644 jellyfish/storage.cc
delete mode 100644 jellyfish/test_double_fifo_input.cc
delete mode 100644 jellyfish/test_read_parser.cc
delete mode 100644 jellyfish/toFloat.h
delete mode 100644 jellyfish/yaggo.cpp
delete mode 100644 jellyfish/yaggo.hpp
rename {jellyfish => lib}/allocators_mmap.cc (51%)
rename {jellyfish => lib}/err.cc (84%)
create mode 100644 lib/generator_manager.cc
create mode 100644 lib/int128.cc
create mode 100644 lib/jsoncpp.cpp
rename jellyfish/hash_function.hpp => lib/mer_dna.cc (71%)
rename {jellyfish => lib}/misc.cc (65%)
create mode 100644 lib/rectangular_binary_matrix.cc
create mode 100644 lib/storage.cc
rename {jellyfish => lib}/thread_exec.cc (77%)
rename {jellyfish => lib}/time.cc (100%)
create mode 100644 local.mk
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