[med-svn] [kmc] branch master updated (2d6d22b -> 64395d5)
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Mon Aug 24 21:25:06 UTC 2015
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a change to branch master
in repository kmc.
from 2d6d22b Upload to unstable
new 941c4f5 start 2.1.1
new 2f7cba5 Imported Upstream version 2.1.1
new 7844cc5 Merge tag 'upstream/2.1.1'
new 9a22fc7 cosmetics
new 13afcd8 patches
new 4fda362 add patches
new 3c56eb5 update version
new 2169066 Imported Upstream version 2.2
new 4f0e841 Merge tag 'upstream/2.2'
new 1b12542 patches
new cf30e28 finalize new patches
new ae0f153 improve description
new deb5e74 add metadata for citation
new b02dea4 update changelog
new 64395d5 update copyright
The 15 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:
.gitattributes | 22 +
.gitignore | 43 +
API.pdf | Bin 0 -> 220319 bytes
LICENSE | 674 -----
README.md | 81 +-
debian/changelog | 9 +
debian/control | 27 +-
debian/copyright | 6 +-
debian/patches/allow-dry-clean | 34 +
...-libz2-include-statements-to-native-debian-libs | 40 +-
...hange-kmc-zlib-and-libz2-to-deb-zlib-and-libbz2 | 20 +-
debian/patches/disable-asmlib | 35 +
debian/patches/hardening | 33 +
.../remove-all-zlib-libz2-include-statements | 20 +-
.../patches/remove-call-to-asmlib-sub-in-kbsorter | 16 +-
debian/patches/remove-references-to-asmlib | 42 +-
.../patches/remove-use-of-asmlib-subroutines.patch | 198 +-
debian/patches/series | 10 +-
debian/patches/use-shared-libs | 59 +
debian/upstream/metadata | 21 +-
debian/watch | 4 +-
kmc_api/kmc_file.cpp | 1760 ++++++++-----
kmc_api/kmc_file.h | 263 +-
kmc_api/kmer_api.cpp | 71 +-
kmc_api/kmer_api.h | 1135 ++++----
kmc_api/kmer_defs.h | 101 +-
kmc_api/mmer.cpp | 98 +-
kmc_api/mmer.h | 362 +--
kmc_api/stdafx.h | 0
kmc_dump/ReadMe.txt | 40 -
kmc_dump/kmc_dump.cpp | 299 +--
kmc_dump/kmc_dump.vcxproj | 336 +--
kmc_dump/nc_utils.cpp | 38 +-
kmc_dump/nc_utils.h | 274 +-
kmc_dump/stdafx.cpp | 16 +-
kmc_dump/stdafx.h | 37 +-
kmc_dump/targetver.h | 16 +-
kmc_dump_sample/ReadMe.txt | 40 -
kmc_dump_sample/kmc_dump_sample.cpp | 275 +-
kmc_dump_sample/kmc_dump_sample.vcxproj | 332 +--
kmc_dump_sample/stdafx.cpp | 16 +-
kmc_dump_sample/stdafx.h | 37 +-
kmc_dump_sample/targetver.h | 16 +-
kmer_counter.sln | 124 +-
kmer_counter/ReadMe.txt | 40 -
kmer_counter/{kmer.cpp => asmlib_wrapper.h} | 40 +-
kmer_counter/bkb_merger.h | 280 ++
kmer_counter/bkb_reader.cpp | 100 +
kmer_counter/bkb_reader.h | 51 +
kmer_counter/bkb_sorter.h | 577 +++++
kmer_counter/bkb_subbin.h | 151 ++
kmer_counter/bkb_uncompactor.h | 688 +++++
kmer_counter/bkb_writer.cpp | 142 +
kmer_counter/bkb_writer.h | 52 +
kmer_counter/defs.h | 265 +-
kmer_counter/develop.cpp | 142 +
kmer_counter/develop.h | 16 +
kmer_counter/fastq_reader.cpp | 949 ++++---
kmer_counter/fastq_reader.h | 246 +-
kmer_counter/kb_collector.h | 454 ++--
kmer_counter/kb_completer.cpp | 586 +++--
kmer_counter/kb_completer.h | 160 +-
kmer_counter/kb_reader.h | 471 ++--
kmer_counter/kb_sorter.h | 2717 ++++++++++----------
kmer_counter/kb_storer.cpp | 536 ++--
kmer_counter/kb_storer.h | 183 +-
kmer_counter/kmc.h | 1763 +++++++------
kmer_counter/kmer.cpp | 36 +-
kmer_counter/kmer.h | 2098 +++++++--------
kmer_counter/kmer_counter.cpp | 854 +++---
kmer_counter/kmer_counter.vcxproj | 465 ++--
kmer_counter/kxmer_set.h | 234 +-
kmer_counter/mem_disk_file.cpp | 226 +-
kmer_counter/mem_disk_file.h | 85 +-
kmer_counter/meta_oper.h | 90 +-
kmer_counter/mmer.cpp | 98 +-
kmer_counter/mmer.h | 362 +--
kmer_counter/params.h | 357 +--
kmer_counter/queues.h | 2336 ++++++++++-------
kmer_counter/radix.cpp | 584 ++---
kmer_counter/radix.h | 87 +-
kmer_counter/rev_byte.cpp | 28 +-
kmer_counter/rev_byte.h | 56 +-
kmer_counter/s_mapper.h | 324 ++-
kmer_counter/splitter.h | 1882 +++++++-------
kmer_counter/stdafx.cpp | 16 +-
kmer_counter/stdafx.h | 43 +-
kmer_counter/targetver.h | 16 +-
kmer_counter/timer.cpp | 122 +-
kmer_counter/timer.h | 116 +-
kmer_counter/x64/Release/kmer.obj | Bin 0 -> 680826 bytes
makefile | 54 +-
makefile_mac | 64 +
readme.txt | 60 +
94 files changed, 15848 insertions(+), 12534 deletions(-)
create mode 100644 .gitattributes
create mode 100644 .gitignore
create mode 100644 API.pdf
delete mode 100644 LICENSE
create mode 100644 debian/patches/allow-dry-clean
create mode 100644 debian/patches/disable-asmlib
create mode 100644 debian/patches/hardening
create mode 100644 debian/patches/use-shared-libs
mode change 100755 => 100644 kmc_api/kmc_file.cpp
mode change 100755 => 100644 kmc_api/kmc_file.h
mode change 100755 => 100644 kmc_api/kmer_api.cpp
mode change 100755 => 100644 kmc_api/kmer_api.h
mode change 100755 => 100644 kmc_api/kmer_defs.h
mode change 100755 => 100644 kmc_api/mmer.cpp
mode change 100755 => 100644 kmc_api/mmer.h
mode change 100755 => 100644 kmc_api/stdafx.h
delete mode 100755 kmc_dump/ReadMe.txt
mode change 100755 => 100644 kmc_dump/kmc_dump.cpp
mode change 100755 => 100644 kmc_dump/kmc_dump.vcxproj
mode change 100755 => 100644 kmc_dump/nc_utils.cpp
mode change 100755 => 100644 kmc_dump/nc_utils.h
mode change 100755 => 100644 kmc_dump/stdafx.cpp
mode change 100755 => 100644 kmc_dump/stdafx.h
mode change 100755 => 100644 kmc_dump/targetver.h
delete mode 100755 kmc_dump_sample/ReadMe.txt
mode change 100755 => 100644 kmc_dump_sample/kmc_dump_sample.cpp
mode change 100755 => 100644 kmc_dump_sample/kmc_dump_sample.vcxproj
mode change 100755 => 100644 kmc_dump_sample/stdafx.cpp
mode change 100755 => 100644 kmc_dump_sample/stdafx.h
mode change 100755 => 100644 kmc_dump_sample/targetver.h
mode change 100755 => 100644 kmer_counter.sln
delete mode 100755 kmer_counter/ReadMe.txt
copy kmer_counter/{kmer.cpp => asmlib_wrapper.h} (53%)
mode change 100755 => 100644
create mode 100644 kmer_counter/bkb_merger.h
create mode 100644 kmer_counter/bkb_reader.cpp
create mode 100644 kmer_counter/bkb_reader.h
create mode 100644 kmer_counter/bkb_sorter.h
create mode 100644 kmer_counter/bkb_subbin.h
create mode 100644 kmer_counter/bkb_uncompactor.h
create mode 100644 kmer_counter/bkb_writer.cpp
create mode 100644 kmer_counter/bkb_writer.h
mode change 100755 => 100644 kmer_counter/defs.h
create mode 100644 kmer_counter/develop.cpp
create mode 100644 kmer_counter/develop.h
mode change 100755 => 100644 kmer_counter/fastq_reader.cpp
mode change 100755 => 100644 kmer_counter/fastq_reader.h
mode change 100755 => 100644 kmer_counter/kb_collector.h
mode change 100755 => 100644 kmer_counter/kb_completer.cpp
mode change 100755 => 100644 kmer_counter/kb_completer.h
mode change 100755 => 100644 kmer_counter/kb_reader.h
mode change 100755 => 100644 kmer_counter/kb_sorter.h
mode change 100755 => 100644 kmer_counter/kb_storer.cpp
mode change 100755 => 100644 kmer_counter/kb_storer.h
mode change 100755 => 100644 kmer_counter/kmc.h
mode change 100755 => 100644 kmer_counter/kmer.cpp
mode change 100755 => 100644 kmer_counter/kmer.h
mode change 100755 => 100644 kmer_counter/kmer_counter.cpp
mode change 100755 => 100644 kmer_counter/kmer_counter.vcxproj
mode change 100755 => 100644 kmer_counter/kxmer_set.h
mode change 100755 => 100644 kmer_counter/mem_disk_file.cpp
mode change 100755 => 100644 kmer_counter/mem_disk_file.h
mode change 100755 => 100644 kmer_counter/meta_oper.h
mode change 100755 => 100644 kmer_counter/mmer.cpp
mode change 100755 => 100644 kmer_counter/mmer.h
mode change 100755 => 100644 kmer_counter/params.h
mode change 100755 => 100644 kmer_counter/queues.h
mode change 100755 => 100644 kmer_counter/radix.cpp
mode change 100755 => 100644 kmer_counter/radix.h
mode change 100755 => 100644 kmer_counter/rev_byte.cpp
mode change 100755 => 100644 kmer_counter/rev_byte.h
mode change 100755 => 100644 kmer_counter/s_mapper.h
mode change 100755 => 100644 kmer_counter/splitter.h
mode change 100755 => 100644 kmer_counter/stdafx.cpp
mode change 100755 => 100644 kmer_counter/stdafx.h
mode change 100755 => 100644 kmer_counter/targetver.h
mode change 100755 => 100644 kmer_counter/timer.cpp
mode change 100755 => 100644 kmer_counter/timer.h
create mode 100644 kmer_counter/x64/Release/kmer.obj
mode change 100755 => 100644 makefile
create mode 100644 makefile_mac
create mode 100644 readme.txt
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