[med-svn] [jellyfish1] branch upstream updated (62af77d -> 379377e)
Andreas Tille
tille at debian.org
Thu Jul 20 07:44:27 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository jellyfish1.
from 62af77d Imported Upstream version 1.1.5
new 379377e New upstream version 1.1.11
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:
Makefile.am | 144 +-
Makefile.in | 1259 +-
aclocal.m4 | 106 +-
config.guess | 449 +-
config.h.in | 9 +
config.sub | 227 +-
configure | 16036 +++++++++----------
configure.ac | 30 +-
depcomp | 190 +-
gtest.mk | 13 +-
install-sh | 29 +-
jellyfish-1.1.pc.in | 2 +-
jellyfish/allocators_malloc.hpp | 2 +-
jellyfish/allocators_mmap.hpp | 2 +-
jellyfish/allocators_shm.hpp | 2 +-
jellyfish/capped_integer.hpp | 6 +-
jellyfish/circular_buffer.hpp | 2 +-
jellyfish/cite.cc | 3 +-
jellyfish/compacted_hash.hpp | 88 +-
jellyfish/concurrent_queues.hpp | 203 +-
jellyfish/count_main_cmdline.hpp | 363 +-
jellyfish/dbg.cc | 7 +
jellyfish/dbg.hpp | 2 +-
jellyfish/direct_indexing_array.hpp | 6 +-
jellyfish/direct_sorted_dumper.hpp | 22 +-
jellyfish/divisor.hpp | 144 +-
jellyfish/dna_codes.hpp | 20 +-
jellyfish/double_fifo_input.hpp | 2 +-
jellyfish/dump_main.cc | 53 +-
jellyfish/dumper.hpp | 25 +-
jellyfish/err.hpp | 41 +-
jellyfish/fastq_dumper.hpp | 2 +-
jellyfish/file_parser.cc | 4 +-
jellyfish/floats.hpp | 13 +-
jellyfish/generate_sequence.cc | 2 +-
jellyfish/half.h | 2 +-
jellyfish/hash.hpp | 13 +-
jellyfish/hash_fastq_merge.cc | 2 +-
jellyfish/hash_merge.cc | 2 +-
jellyfish/heap.hpp | 4 +-
jellyfish/invertible_hash_array.hpp | 167 +-
jellyfish/locking_hash_counters.hpp | 4 +-
jellyfish/locks_pthread.hpp | 6 +-
jellyfish/mapped_file.hpp | 6 +-
jellyfish/mer_counter.cc | 58 +-
jellyfish/misc.cc | 13 +
jellyfish/misc.hpp | 2 +
jellyfish/offsets_key_value.hpp | 68 +-
jellyfish/parse_dna.hpp | 2 +-
jellyfish/parse_qual_dna.hpp | 4 +-
jellyfish/parse_read.hpp | 8 +-
jellyfish/randomc.h | 4 +-
jellyfish/raw_dumper.hpp | 26 +-
jellyfish/simple_circular_buffer.hpp | 134 +
jellyfish/simple_growing_array.hpp | 2 +-
jellyfish/sorted_dumper.hpp | 43 +-
jellyfish/square_binary_matrix.cc | 18 +-
jellyfish/square_binary_matrix.hpp | 15 +-
jellyfish/test_double_fifo_input.cc | 2 +-
jellyfish/time.hpp | 6 +-
jellyfish/yaggo.hpp | 4 +-
ltmain.sh | 4017 +++--
m4/gnulib-cache.m4 | 35 -
m4/libtool.m4 | 2248 ++-
m4/ltoptions.m4 | 32 +-
m4/ltversion.m4 | 12 +-
m4/lt~obsolete.m4 | 12 +-
missing | 53 +-
tests/compat.sh.in | 2 +-
tests/parallel_direct_indexing.sh | 23 +-
tests/parallel_fastq_direct_indexing.sh | 28 +
tests/parallel_fastq_hashing.sh | 16 +-
tests/parallel_hashing.sh | 37 +-
.../gtest/include/gtest/internal/gtest-internal.h | 10 +
.../gtest/include/gtest/internal/gtest-port.h | 10 +
.../gtest/include/gtest/internal/gtest-string.h | 10 +
unit_tests/gtest/src/gtest-port.cc | 6 +
unit_tests/test_offsets_key_value.cc | 288 +-
unit_tests/test_simple_circular_buffer.cc | 71 +
unit_tests/test_square_binary_matrix.cc | 133 +
unit_tests/unit_tests.sh | 2 +-
81 files changed, 14813 insertions(+), 12355 deletions(-)
create mode 100644 jellyfish/simple_circular_buffer.hpp
mode change 100755 => 100644 ltmain.sh
delete mode 100644 m4/gnulib-cache.m4
create mode 100644 tests/parallel_fastq_direct_indexing.sh
create mode 100644 unit_tests/test_simple_circular_buffer.cc
create mode 100644 unit_tests/test_square_binary_matrix.cc
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