[med-svn] [crac] branch master updated (3c80cc2 -> e0c393e)
Andreas Tille
tille at debian.org
Sat Sep 10 22:04:29 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository crac.
from 3c80cc2 New publication
new 4311504 Use Debian packaged libgzstream and libjellyfish
new 93f464c Need to strip third party sources from upstream source
new 5a048c1 New upstream version 2.5.0+dfsg
new e0c393e Merge tag 'upstream/2.5.0+dfsg'
The 4 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:
debian/changelog | 2 +-
debian/control | 6 +-
debian/copyright | 2 +
debian/rules | 2 +-
debian/watch | 3 +-
src/libJellyfish-2.0/HalfLICENSE | 34 -
src/libJellyfish-2.0/LICENSE | 674 -
src/libJellyfish-2.0/Makefile.am | 206 -
src/libJellyfish-2.0/Makefile.in | 1410 --
src/libJellyfish-2.0/README | 98 -
src/libJellyfish-2.0/aclocal.m4 | 1369 --
src/libJellyfish-2.0/compile | 347 -
src/libJellyfish-2.0/config.guess | 1420 --
src/libJellyfish-2.0/config.h.in | 89 -
src/libJellyfish-2.0/config.sub | 1794 --
src/libJellyfish-2.0/configure | 18411 -----------------
src/libJellyfish-2.0/configure.ac | 100 -
src/libJellyfish-2.0/depcomp | 791 -
src/libJellyfish-2.0/doc/jellyfish.man | 647 -
src/libJellyfish-2.0/doc/jellyfish.pdf | Bin 242134 -> 0 bytes
src/libJellyfish-2.0/gtest.mk | 18 -
.../include/jellyfish/allocators_mmap.hpp | 78 -
.../include/jellyfish/atomic_bits_array.hpp | 196 -
.../include/jellyfish/atomic_field.hpp | 157 -
.../include/jellyfish/atomic_gcc.hpp | 68 -
.../include/jellyfish/backtrace.hpp | 18 -
.../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 -
src/libJellyfish-2.0/include/jellyfish/divisor.hpp | 150 -
src/libJellyfish-2.0/include/jellyfish/dumper.hpp | 103 -
src/libJellyfish-2.0/include/jellyfish/err.hpp | 133 -
.../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 -
src/libJellyfish-2.0/include/jellyfish/int128.hpp | 203 -
.../include/jellyfish/jellyfish.hpp | 42 -
src/libJellyfish-2.0/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 -
src/libJellyfish-2.0/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 -
.../jellyfish/mer_overlap_sequence_parser.hpp | 279 -
.../include/jellyfish/mer_qual_iterator.hpp | 118 -
src/libJellyfish-2.0/include/jellyfish/misc.hpp | 247 -
.../include/jellyfish/offsets_key_value.hpp | 277 -
.../jellyfish/rectangular_binary_matrix.hpp | 379 -
.../include/jellyfish/simple_circular_buffer.hpp | 134 -
.../include/jellyfish/sorted_dumper.hpp | 115 -
.../include/jellyfish/stdio_filebuf.hpp | 170 -
src/libJellyfish-2.0/include/jellyfish/storage.hpp | 37 -
.../include/jellyfish/stream_iterator.hpp | 90 -
.../include/jellyfish/stream_manager.hpp | 158 -
.../include/jellyfish/text_dumper.hpp | 88 -
.../include/jellyfish/thread_exec.hpp | 53 -
src/libJellyfish-2.0/include/jellyfish/time.hpp | 92 -
.../include/jellyfish/token_ring.hpp | 87 -
.../include/jellyfish/whole_sequence_parser.hpp | 150 -
src/libJellyfish-2.0/install-sh | 527 -
src/libJellyfish-2.0/jellyfish-2.0.pc.in | 10 -
src/libJellyfish-2.0/jellyfish/dbg.hpp | 153 -
src/libJellyfish-2.0/jellyfish/fstream_default.hpp | 68 -
src/libJellyfish-2.0/jellyfish/merge_files.hpp | 30 -
src/libJellyfish-2.0/jellyfish/randomc.h | 198 -
src/libJellyfish-2.0/lib/allocators_mmap.cc | 114 -
src/libJellyfish-2.0/lib/err.cc | 31 -
src/libJellyfish-2.0/lib/generator_manager.cc | 282 -
src/libJellyfish-2.0/lib/int128.cc | 94 -
src/libJellyfish-2.0/lib/jsoncpp.cpp | 4230 ----
src/libJellyfish-2.0/lib/mer_dna.cc | 23 -
src/libJellyfish-2.0/lib/misc.cc | 102 -
.../lib/rectangular_binary_matrix.cc | 216 -
src/libJellyfish-2.0/lib/storage.cc | 51 -
src/libJellyfish-2.0/lib/thread_exec.cc | 44 -
src/libJellyfish-2.0/lib/time.cc | 19 -
src/libJellyfish-2.0/ltmain.sh | 9661 ---------
src/libJellyfish-2.0/m4/libtool.m4 | 7997 --------
src/libJellyfish-2.0/m4/ltoptions.m4 | 384 -
src/libJellyfish-2.0/m4/ltsugar.m4 | 123 -
src/libJellyfish-2.0/m4/ltversion.m4 | 23 -
src/libJellyfish-2.0/m4/lt~obsolete.m4 | 98 -
src/libJellyfish-2.0/missing | 215 -
src/libJellyfish-2.0/unit_tests/gtest/gtest.h | 20061 -------------------
.../unit_tests/gtest/src/gtest-all.cc | 9592 ---------
.../unit_tests/gtest/src/gtest_main.cc | 38 -
src/libgzstream/COPYING.LIB | 504 -
src/libgzstream/Makefile.am | 107 -
src/libgzstream/Makefile.in | 709 -
src/libgzstream/README | 6 -
src/libgzstream/gzstream.cpp | 165 -
src/libgzstream/gzstream.h | 121 -
102 files changed, 10 insertions(+), 94054 deletions(-)
delete mode 100644 src/libJellyfish-2.0/HalfLICENSE
delete mode 100644 src/libJellyfish-2.0/LICENSE
delete mode 100644 src/libJellyfish-2.0/Makefile.am
delete mode 100644 src/libJellyfish-2.0/Makefile.in
delete mode 100644 src/libJellyfish-2.0/README
delete mode 100644 src/libJellyfish-2.0/aclocal.m4
delete mode 100755 src/libJellyfish-2.0/compile
delete mode 100755 src/libJellyfish-2.0/config.guess
delete mode 100644 src/libJellyfish-2.0/config.h.in
delete mode 100755 src/libJellyfish-2.0/config.sub
delete mode 100755 src/libJellyfish-2.0/configure
delete mode 100644 src/libJellyfish-2.0/configure.ac
delete mode 100755 src/libJellyfish-2.0/depcomp
delete mode 100644 src/libJellyfish-2.0/doc/jellyfish.man
delete mode 100644 src/libJellyfish-2.0/doc/jellyfish.pdf
delete mode 100755 src/libJellyfish-2.0/gtest.mk
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/allocators_mmap.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/atomic_bits_array.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/atomic_field.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/atomic_gcc.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/backtrace.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/binary_dumper.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/bloom_common.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/bloom_counter2.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/bloom_filter.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/circular_buffer.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/compare_and_swap.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/cooperative_pool.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/cooperative_pool2.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/cpp_array.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/divisor.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/dumper.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/err.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/file_header.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/generator_manager.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/generic_file_header.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/hash_counter.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/int128.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/jellyfish.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/json.h
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/large_hash_array.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/large_hash_iterator.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/locks_pthread.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/mapped_file.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_dna.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_dna_bloom_counter.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_heap.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_iterator.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_overlap_sequence_parser.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/mer_qual_iterator.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/misc.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/offsets_key_value.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/rectangular_binary_matrix.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/simple_circular_buffer.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/sorted_dumper.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/stdio_filebuf.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/storage.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/stream_iterator.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/stream_manager.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/text_dumper.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/thread_exec.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/time.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/token_ring.hpp
delete mode 100644 src/libJellyfish-2.0/include/jellyfish/whole_sequence_parser.hpp
delete mode 100755 src/libJellyfish-2.0/install-sh
delete mode 100644 src/libJellyfish-2.0/jellyfish-2.0.pc.in
delete mode 100644 src/libJellyfish-2.0/jellyfish/dbg.hpp
delete mode 100644 src/libJellyfish-2.0/jellyfish/fstream_default.hpp
delete mode 100644 src/libJellyfish-2.0/jellyfish/merge_files.hpp
delete mode 100644 src/libJellyfish-2.0/jellyfish/randomc.h
delete mode 100644 src/libJellyfish-2.0/lib/allocators_mmap.cc
delete mode 100644 src/libJellyfish-2.0/lib/err.cc
delete mode 100644 src/libJellyfish-2.0/lib/generator_manager.cc
delete mode 100644 src/libJellyfish-2.0/lib/int128.cc
delete mode 100644 src/libJellyfish-2.0/lib/jsoncpp.cpp
delete mode 100644 src/libJellyfish-2.0/lib/mer_dna.cc
delete mode 100644 src/libJellyfish-2.0/lib/misc.cc
delete mode 100644 src/libJellyfish-2.0/lib/rectangular_binary_matrix.cc
delete mode 100644 src/libJellyfish-2.0/lib/storage.cc
delete mode 100644 src/libJellyfish-2.0/lib/thread_exec.cc
delete mode 100644 src/libJellyfish-2.0/lib/time.cc
delete mode 100644 src/libJellyfish-2.0/ltmain.sh
delete mode 100644 src/libJellyfish-2.0/m4/libtool.m4
delete mode 100644 src/libJellyfish-2.0/m4/ltoptions.m4
delete mode 100644 src/libJellyfish-2.0/m4/ltsugar.m4
delete mode 100644 src/libJellyfish-2.0/m4/ltversion.m4
delete mode 100644 src/libJellyfish-2.0/m4/lt~obsolete.m4
delete mode 100755 src/libJellyfish-2.0/missing
delete mode 100644 src/libJellyfish-2.0/unit_tests/gtest/gtest.h
delete mode 100644 src/libJellyfish-2.0/unit_tests/gtest/src/gtest-all.cc
delete mode 100644 src/libJellyfish-2.0/unit_tests/gtest/src/gtest_main.cc
delete mode 100644 src/libgzstream/COPYING.LIB
delete mode 100644 src/libgzstream/Makefile.am
delete mode 100644 src/libgzstream/Makefile.in
delete mode 100644 src/libgzstream/README
delete mode 100644 src/libgzstream/gzstream.cpp
delete mode 100644 src/libgzstream/gzstream.h
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