[med-svn] [jellyfish1] branch master updated (219028e -> 9a43de2)
Andreas Tille
tille at debian.org
Tue Nov 17 09:02:59 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository jellyfish1.
from 219028e New upstream version, point to new location on Github, we are tracking jellyfish version 1 now
new 1469d4e Remove .gitignore
new 16713c5 Imported Upstream version 1.5.5
new 266ef0b Merge tag 'upstream/1.5.5'
new 8eae1e6 cme fix dpkg-control
new 48d7d1d Add paragraph to description why we are packaging version 1
new 2261e85 Bump changed date
new e0b93ab Adapt build to new upstream version
new 9a43de2 Cheating with tests ...
The 8 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 | 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 +-
debian/changelog | 3 +-
debian/control | 12 +-
.../a3c491af4b02086cf13269eb5df8266a748e1c7c.patch | 30 +
debian/patches/series | 1 +
debian/rules | 8 +-
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 | 21 +
{jellyfish => sub_commands}/jellyfish.cc | 18 +-
sub_commands/mem_main.cc | 54 +
sub_commands/mem_main_cmdline.yaggo | 121 +
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 +-
327 files changed, 55873 insertions(+), 102998 deletions(-)
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
create mode 100644 debian/patches/a3c491af4b02086cf13269eb5df8266a748e1c7c.patch
create mode 100644 debian/patches/series
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
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