[med-svn] [kmc] 03/05: Merge tag 'upstream/2.3+dfsg'
Sascha Steinbiss
sascha at steinbiss.name
Sat Dec 19 22:47:43 UTC 2015
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sascha-guest pushed a commit to branch master
in repository kmc.
commit a5697f1207cef0f7ef7fe3b17c442f49c83176b9
Merge: db19e29 d1443ec
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sat Dec 19 14:54:53 2015 +0000
Merge tag 'upstream/2.3+dfsg'
Upstream version 2.3+dfsg
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 | 135 +-
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_tools/stdafx.cpp | 8 +
kmc_tools/stdafx.h | 17 +
kmc_tools/targetver.h | 8 +
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 +-
111 files changed, 12317 insertions(+), 556 deletions(-)
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