[med-svn] [kmc] branch master updated (6325dec -> 3df6ba1)
Sascha Steinbiss
sascha at steinbiss.name
Sat Dec 19 22:47:42 UTC 2015
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sascha-guest pushed a change to branch master
in repository kmc.
from 6325dec Minor fixes to d/control descriptions
new db19e29 version bump
new d1443ec Imported Upstream version 2.3+dfsg
new a5697f1 Merge tag 'upstream/2.3+dfsg'
new b605597 new upstream release
new 3df6ba1 add TODO item for remaining man page work
The 5 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 | 9 +-
...005-Add-static-library-target-to-makefile.patch | 49 +-
...e-standard-compiler-environment-variables.patch | 60 +-
debian/patches/disable-asmlib | 37 +-
debian/patches/hardening | 35 +-
debian/patches/series | 2 -
debian/patches/use-shared-libs | 27 +-
kmc_api/kmc_file.cpp | 405 ++++-
kmc_api/kmc_file.h | 53 +-
kmc_api/kmer_api.cpp | 4 +-
kmc_api/kmer_api.h | 40 +-
kmc_api/kmer_defs.h | 8 +-
kmc_api/mmer.cpp | 4 +-
kmc_api/mmer.h | 4 +-
kmc_dump/kmc_dump.cpp | 8 +-
kmc_dump/nc_utils.cpp | 4 +-
kmc_dump/nc_utils.h | 4 +-
kmc_dump_sample/kmc_dump_sample.cpp | 6 +-
kmc_tools.pdf | Bin 0 -> 132755 bytes
{kmer_counter => kmc_tools}/asmlib_wrapper.h | 7 +-
kmc_tools/bundle.h | 233 +++
kmc_tools/config.h | 550 ++++++
kmc_tools/defs.h | 92 ++
kmc_tools/dump_writer.h | 174 ++
kmc_tools/expression_node.h | 198 +++
kmc_tools/fastq_filter.cpp | 364 ++++
kmc_tools/fastq_filter.h | 83 +
{kmer_counter => kmc_tools}/fastq_reader.cpp | 157 +-
{kmer_counter => kmc_tools}/fastq_reader.h | 53 +-
kmc_tools/fastq_writer.cpp | 69 +
kmc_tools/fastq_writer.h | 43 +
kmc_tools/histogram_writer.h | 54 +
kmc_tools/kmc1_db_reader.h | 379 +++++
kmc_tools/kmc1_db_writer.h | 380 +++++
kmc_tools/kmc2_db_reader.h | 1398 ++++++++++++++++
kmc_tools/kmc_header.cpp | 88 +
kmc_tools/kmc_header.h | 55 +
kmc_tools/kmc_tools.cpp | 360 ++++
.../kmc_tools.vcxproj | 79 +-
kmc_tools/kmer.h | 522 ++++++
kmc_tools/libs/alibcof64.lib | Bin 0 -> 45248 bytes
kmc_tools/libs/alibelf64.a | Bin 0 -> 61206 bytes
kmc_tools/libs/asmlib.h | 265 +++
kmc_tools/libs/bzlib.h | 282 ++++
kmc_tools/libs/bzlib_private.h | 509 ++++++
kmc_tools/libs/libamac64.a | Bin 0 -> 51960 bytes
kmc_tools/libs/libbz2.1.0.5.dylib | Bin 0 -> 16696 bytes
kmc_tools/libs/libbz2.a | Bin 0 -> 349570 bytes
kmc_tools/libs/libbzip2.lib | Bin 0 -> 290012 bytes
kmc_tools/libs/libz.1.2.5.dylib | Bin 0 -> 17592 bytes
kmc_tools/libs/libz.a | Bin 0 -> 134978 bytes
kmc_tools/libs/zconf.h | 506 ++++++
kmc_tools/libs/zlib.h | 1744 ++++++++++++++++++++
kmc_tools/libs/zlibstat.lib | Bin 0 -> 768146 bytes
{kmer_counter => kmc_tools}/meta_oper.h | 18 +-
kmc_tools/nc_utils.cpp | 17 +
{kmc_dump => kmc_tools}/nc_utils.h | 34 +-
kmc_tools/operations.h | 284 ++++
kmc_tools/output_parser.h | 174 ++
kmc_tools/parameters_parser.cpp | 536 ++++++
kmc_tools/parameters_parser.h | 111 ++
kmc_tools/parser.cpp | 184 +++
kmc_tools/parser.h | 107 ++
kmc_tools/percent_progress.cpp | 93 ++
kmc_tools/percent_progress.h | 48 +
kmc_tools/queues.h | 393 +++++
{kmc_dump => kmc_tools}/stdafx.cpp | 2 +-
{kmc_dump => kmc_tools}/stdafx.h | 0
{kmc_dump => kmc_tools}/targetver.h | 0
kmc_tools/timer.h | 33 +
kmc_tools/tokenizer.cpp | 77 +
kmc_tools/tokenizer.h | 39 +
kmer_counter.sln | 13 +
kmer_counter/asmlib_wrapper.h | 4 +-
kmer_counter/bkb_merger.h | 8 +-
kmer_counter/bkb_reader.cpp | 4 +-
kmer_counter/bkb_reader.h | 4 +-
kmer_counter/bkb_sorter.h | 8 +-
kmer_counter/bkb_subbin.h | 4 +-
kmer_counter/bkb_uncompactor.h | 4 +-
kmer_counter/bkb_writer.cpp | 4 +-
kmer_counter/bkb_writer.h | 4 +-
kmer_counter/defs.h | 13 +-
kmer_counter/fastq_reader.cpp | 4 +-
kmer_counter/fastq_reader.h | 4 +-
kmer_counter/kb_collector.h | 4 +-
kmer_counter/kb_completer.cpp | 18 +-
kmer_counter/kb_completer.h | 216 ++-
kmer_counter/kb_reader.h | 8 +-
kmer_counter/kb_sorter.h | 93 +-
kmer_counter/kb_storer.cpp | 4 +-
kmer_counter/kb_storer.h | 4 +-
kmer_counter/kmc.h | 256 ++-
kmer_counter/kmer.cpp | 4 +-
kmer_counter/kmer.h | 4 +-
kmer_counter/kmer_counter.cpp | 23 +-
kmer_counter/kmer_counter.vcxproj | 5 +-
kmer_counter/kxmer_set.h | 4 +-
kmer_counter/mem_disk_file.cpp | 4 +-
kmer_counter/mem_disk_file.h | 4 +-
kmer_counter/meta_oper.h | 4 +-
kmer_counter/mmer.cpp | 4 +-
kmer_counter/mmer.h | 4 +-
kmer_counter/params.h | 18 +-
kmer_counter/prob_qual.cpp | 67 +
kmer_counter/prob_qual.h | 20 +
kmer_counter/queues.h | 20 +-
kmer_counter/radix.cpp | 4 +-
kmer_counter/radix.h | 4 +-
kmer_counter/rev_byte.cpp | 4 +-
kmer_counter/rev_byte.h | 4 +-
kmer_counter/s_mapper.h | 4 +-
kmer_counter/small_k_buf.h | 43 +
kmer_counter/splitter.h | 422 ++++-
kmer_counter/timer.cpp | 4 +-
kmer_counter/timer.h | 4 +-
makefile | 46 +-
makefile_mac | 47 +-
118 files changed, 12394 insertions(+), 611 deletions(-)
create mode 100644 kmc_tools.pdf
copy {kmer_counter => kmc_tools}/asmlib_wrapper.h (74%)
create mode 100644 kmc_tools/bundle.h
create mode 100644 kmc_tools/config.h
create mode 100644 kmc_tools/defs.h
create mode 100644 kmc_tools/dump_writer.h
create mode 100644 kmc_tools/expression_node.h
create mode 100644 kmc_tools/fastq_filter.cpp
create mode 100644 kmc_tools/fastq_filter.h
copy {kmer_counter => kmc_tools}/fastq_reader.cpp (65%)
copy {kmer_counter => kmc_tools}/fastq_reader.h (58%)
create mode 100644 kmc_tools/fastq_writer.cpp
create mode 100644 kmc_tools/fastq_writer.h
create mode 100644 kmc_tools/histogram_writer.h
create mode 100644 kmc_tools/kmc1_db_reader.h
create mode 100644 kmc_tools/kmc1_db_writer.h
create mode 100644 kmc_tools/kmc2_db_reader.h
create mode 100644 kmc_tools/kmc_header.cpp
create mode 100644 kmc_tools/kmc_header.h
create mode 100644 kmc_tools/kmc_tools.cpp
copy kmc_dump/kmc_dump.vcxproj => kmc_tools/kmc_tools.vcxproj (70%)
create mode 100644 kmc_tools/kmer.h
create mode 100644 kmc_tools/libs/alibcof64.lib
create mode 100644 kmc_tools/libs/alibelf64.a
create mode 100644 kmc_tools/libs/asmlib.h
create mode 100644 kmc_tools/libs/bzlib.h
create mode 100644 kmc_tools/libs/bzlib_private.h
create mode 100644 kmc_tools/libs/libamac64.a
create mode 100644 kmc_tools/libs/libbz2.1.0.5.dylib
create mode 100644 kmc_tools/libs/libbz2.a
create mode 100644 kmc_tools/libs/libbzip2.lib
create mode 100644 kmc_tools/libs/libz.1.2.5.dylib
create mode 100644 kmc_tools/libs/libz.a
create mode 100644 kmc_tools/libs/zconf.h
create mode 100644 kmc_tools/libs/zlib.h
create mode 100644 kmc_tools/libs/zlibstat.lib
copy {kmer_counter => kmc_tools}/meta_oper.h (64%)
create mode 100644 kmc_tools/nc_utils.cpp
copy {kmc_dump => kmc_tools}/nc_utils.h (79%)
create mode 100644 kmc_tools/operations.h
create mode 100644 kmc_tools/output_parser.h
create mode 100644 kmc_tools/parameters_parser.cpp
create mode 100644 kmc_tools/parameters_parser.h
create mode 100644 kmc_tools/parser.cpp
create mode 100644 kmc_tools/parser.h
create mode 100644 kmc_tools/percent_progress.cpp
create mode 100644 kmc_tools/percent_progress.h
create mode 100644 kmc_tools/queues.h
copy {kmc_dump => kmc_tools}/stdafx.cpp (82%)
copy {kmc_dump => kmc_tools}/stdafx.h (100%)
copy {kmc_dump => kmc_tools}/targetver.h (100%)
create mode 100644 kmc_tools/timer.h
create mode 100644 kmc_tools/tokenizer.cpp
create mode 100644 kmc_tools/tokenizer.h
create mode 100644 kmer_counter/prob_qual.cpp
create mode 100644 kmer_counter/prob_qual.h
create mode 100644 kmer_counter/small_k_buf.h
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