[med-svn] [jellyfish1] branch master updated (71708e3 -> c220063)
Andreas Tille
tille at debian.org
Thu Jul 20 07:44:25 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository jellyfish1.
from 71708e3 Adapt watch file to only fetch 1.x version updates
new 97751ec New upstream version
new 379377e New upstream version 1.1.11
new c220063 Merge tag 'upstream/1.1.11'
The 3 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 +-
debian/changelog | 2 +-
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 +-
82 files changed, 14814 insertions(+), 12356 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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