This is an automated email from the git hooks/post-receive script. jssoares-guest pushed a commit to branch master in repository kmc.
commit 837b07da903e9732e0e8bdd10d2ceaca0f0ec3c6 Author: Jorge Soares <[email protected]> Date: Tue Nov 18 12:53:06 2014 +0000 Imported Upstream version 2.0+dfsg-1 --- debian/changelog | 5 - debian/compat | 1 - debian/control | 39 ------ debian/copyright | 23 ---- debian/kmc.install | 1 - debian/kmc.manpages | 1 - ...-libz2-include-statements-to-native-debian-libs | 30 ----- ...hange-kmc-zlib-and-libz2-to-deb-zlib-and-libbz2 | 18 --- debian/patches/debian-dependent-makefile.patch | 36 ------ .../remove-all-zlib-libz2-include-statements | 15 --- .../patches/remove-call-to-asmlib-sub-in-kbsorter | 16 --- .../remove-embedded-libraries-from-makefile | 26 ---- .../remove-gz-and-bz-flags-from-compilation | 13 -- debian/patches/remove-references-to-asmlib | 44 ------- .../patches/remove-use-of-asmlib-subroutines.patch | 141 --------------------- debian/patches/removing-static-option-in-makefile | 1 - debian/patches/series | 6 - debian/rules | 25 ---- debian/source/format | 1 - debian/upstream/metadata | 12 -- debian/usage_to_man | 140 -------------------- debian/watch | 5 - 22 files changed, 599 deletions(-) diff --git a/debian/changelog b/debian/changelog deleted file mode 100644 index d941639..0000000 --- a/debian/changelog +++ /dev/null @@ -1,5 +0,0 @@ -kmc (2.0+dfsg-1) unstable; urgency=medium - - * Initial release (Closes: #1234) - - -- Jorge Soares <[email protected]> Mon, 03 Nov 2014 14:46:54 +0200 diff --git a/debian/compat b/debian/compat deleted file mode 100644 index ec63514..0000000 --- a/debian/compat +++ /dev/null @@ -1 +0,0 @@ -9 diff --git a/debian/control b/debian/control deleted file mode 100644 index 365cc7a..0000000 --- a/debian/control +++ /dev/null @@ -1,39 +0,0 @@ -Source: kmc -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Andreas Tille <[email protected]>, - Jorge Soares <[email protected]> -Section: science -Priority: optional -Build-Depends: debhelper (>= 9), - zlib1g-dev, - libbz2-dev, - libboost1.54-all-dev, - help2man, - d-shlibs -Standards-Version: 3.9.6 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/kmc.git -Homepage: https://github.com/js21/kmc - -Package: kmc -Architecture: any -Depends: ${shlibs:Depends}, - ${misc:Depends} -Description: Designed for counting k-mers (sequences of consecutive k symbols) - in a set of reads K-mer counting is important for many bioinformatics - applications, e.g., developing de Bruijn graph assemblers. - Building de Bruijn graphs is a commonly used approach for genome - assembly with data from second-generation sequencer. - Unfortunately, sequencing errors (frequent in practice) - results in huge memory requirements for de Bruijn graphs, as well - as long build time. One of the popular approaches to handle this - problem is filtering the input reads in such a way that unique k-mers - (very likely obtained as a result of an error) are discarded. - . - Thus, KMC scans the raw reads and produces a compact representation - of all non-unique reads accompanied with number of their occurrences. - The algorithm implemented in KMC makes use mostly of disk space rather - than RAM, which allows one to use KMC even on rather typical personal - computers. When run at high-end server (what is necessary for KMC - competitors) it outperforms them in both memory requirements and - speed of computation. The disk space necessary for computation is in - order of the size of input data (usually it is smaller). \ No newline at end of file diff --git a/debian/copyright b/debian/copyright deleted file mode 100644 index 2f76f2e..0000000 --- a/debian/copyright +++ /dev/null @@ -1,23 +0,0 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Upstream-Name: KMC -Source: https://github.com/js21/kmc -Files-Excluded: kmer_counter/libs/* - -Files: * -Copyright: © 2012-2013 username <mail address> -License: GPL-3 - This package is free software; you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 3 of the License, or - (at your option) any later version. - . - This package is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - . - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/> - . - On Debian systems, the complete text of the GNU General - Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". diff --git a/debian/kmc.install b/debian/kmc.install deleted file mode 100644 index efa6632..0000000 --- a/debian/kmc.install +++ /dev/null @@ -1 +0,0 @@ -bin/* \ No newline at end of file diff --git a/debian/kmc.manpages b/debian/kmc.manpages deleted file mode 100644 index bf519d7..0000000 --- a/debian/kmc.manpages +++ /dev/null @@ -1 +0,0 @@ -man/*.1 diff --git a/debian/patches/change-all-zlib-libz2-include-statements-to-native-debian-libs b/debian/patches/change-all-zlib-libz2-include-statements-to-native-debian-libs deleted file mode 100644 index 0355fbe..0000000 --- a/debian/patches/change-all-zlib-libz2-include-statements-to-native-debian-libs +++ /dev/null @@ -1,30 +0,0 @@ -Description: zlib and libbz2 are distributed with the KMC. -This patch alters the include statments for these libraries, -using the debian libs instead.--- a/kmer_counter/fastq_reader.h -+++ b/kmer_counter/fastq_reader.h -@@ -16,8 +16,8 @@ - #include <stdio.h> - #include <iostream> - --#include "libs/zlib.h" --#include "libs/bzlib.h" -+#include "zlib.h" -+#include "bzlib.h" - - - using namespace std; -Index: b/kmer_counter/fastq_reader.h -=================================================================== ---- a/kmer_counter/fastq_reader.h -+++ b/kmer_counter/fastq_reader.h -@@ -16,8 +16,8 @@ - #include <stdio.h> - #include <iostream> - --#include "libs/zlib.h" --#include "libs/bzlib.h" -+#include "zlib.h" -+#include "bzlib.h" - - - using namespace std; diff --git a/debian/patches/change-kmc-zlib-and-libz2-to-deb-zlib-and-libbz2 b/debian/patches/change-kmc-zlib-and-libz2-to-deb-zlib-and-libbz2 deleted file mode 100644 index 80091d2..0000000 --- a/debian/patches/change-kmc-zlib-and-libz2-to-deb-zlib-and-libbz2 +++ /dev/null @@ -1,18 +0,0 @@ -Description: KMC distributes zlib and libbz2. -This changes the usage of the distributed libs -and makes KMC use the native debian libs -Index: b/kmer_counter/fastq_reader.h -=================================================================== ---- a/kmer_counter/fastq_reader.h -+++ b/kmer_counter/fastq_reader.h -@@ -16,8 +16,8 @@ - #include <stdio.h> - #include <iostream> - --#include "libs/zlib.h" --#include "libs/bzlib.h" -+#include "zlib.h" -+#include "bzlib.h" - - - using namespace std; diff --git a/debian/patches/debian-dependent-makefile.patch b/debian/patches/debian-dependent-makefile.patch deleted file mode 100644 index 8bb32d4..0000000 --- a/debian/patches/debian-dependent-makefile.patch +++ /dev/null @@ -1,36 +0,0 @@ -Description: Removes all local dependencies from the makefile and -establishes links to the respective debian packages -Index: b/makefile -=================================================================== ---- a/makefile -+++ b/makefile -@@ -1,7 +1,7 @@ - all: kmc -- --BOOST_LIB = /boost/boost_1_55_0/stage/lib --BOOST_H = /boost/boost_1_55_0 -+ -+BOOST_LIB = /usr/lib/x86_64-linux-gnu -+BOOST_H = /usr/include/boost - - KMC_BIN_DIR = bin - KMC_MAIN_DIR = kmer_counter -@@ -13,15 +13,15 @@ CFLAGS = -Wall -O3 -m64 -static -fopenmp - CLINK = -lm -static -fopenmp -O3 -std=c++11 - - .cpp.o: -- $(CC) $(CFLAGS) -c $< -o $@ -+ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< -o $@ - - kmc: $(KMC_MAIN_DIR)/kmer_counter.o $(KMC_MAIN_DIR)/mmer.o $(KMC_MAIN_DIR)/mem_disk_file.o $(KMC_MAIN_DIR)/rev_byte.o $(KMC_MAIN_DIR)/fastq_reader.o $(KMC_MAIN_DIR)/timer.o $(KMC_MAIN_DIR)/radix.o $(KMC_MAIN_DIR)/kb_completer.o $(KMC_MAIN_DIR)/kb_storer.o $(KMC_MAIN_DIR)/kmer.o - -mkdir -p $(KMC_BIN_DIR) -- $(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $(KMC_MAIN_DIR)/kmer_counter.o $(KMC_MAIN_DIR)/mem_disk_file.o $(KMC_MAIN_DIR)/rev_byte.o $(KMC_MAIN_DIR)/mmer.o $(KMC_MAIN_DIR)/fastq_reader.o $(KMC_MAIN_DIR)/timer.o $(KMC_MAIN_DIR)/radix.o $(KMC_MAIN_DIR)/kb_completer.o $(KMC_MAIN_DIR)/kb_storer.o $(KMC_MAIN_DIR)/kmer.o $(KMC_MAIN_DIR)/libs/alibelf64.a $(KMC_MAIN_DIR)/libs/libz.a $(KMC_MAIN_DIR)/libs/libbz2.a $(BOOST_LIB)/libboost_thread.a $(BOOST_LIB)/libboost_filesystem.a $(BOOST_LIB)/libboost_system.a -+ $(CC) $(CPPFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $(KMC_MAIN_DIR)/kmer_counter.o $(KMC_MAIN_DIR)/mem_disk_file.o $(KMC_MAIN_DIR)/rev_byte.o $(KMC_MAIN_DIR)/mmer.o $(KMC_MAIN_DIR)/fastq_reader.o $(KMC_MAIN_DIR)/timer.o $(KMC_MAIN_DIR)/radix.o $(KMC_MAIN_DIR)/kb_completer.o $(KMC_MAIN_DIR)/kb_storer.o $(KMC_MAIN_DIR)/kmer.o $(KMC_MAIN_DIR)/libs/alibelf64.a $(KMC_MAIN_DIR)/libs/libz.a $(KMC_MAIN_DIR)/libs/libbz2.a $(BOOST_LIB)/libboost_thread.a $(BOOST_LIB)/libboost_filesystem.a $(BOOST_LIB [...] - - kmc_dump: $(KMC_DUMP_DIR)/nc_utils.o $(KMC_API_DIR)/mmer.o $(KMC_DUMP_DIR)/kmc_dump.o $(KMC_API_DIR)/kmc_file.o $(KMC_API_DIR)/kmer_api.o - -mkdir -p $(KMC_BIN_DIR) -- $(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $(KMC_DUMP_DIR)/nc_utils.o $(KMC_API_DIR)/mmer.o $(KMC_DUMP_DIR)/kmc_dump.o $(KMC_API_DIR)/kmc_file.o $(KMC_API_DIR)/kmer_api.o -+ $(CC) $(CPPFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $(KMC_DUMP_DIR)/nc_utils.o $(KMC_API_DIR)/mmer.o $(KMC_DUMP_DIR)/kmc_dump.o $(KMC_API_DIR)/kmc_file.o $(KMC_API_DIR)/kmer_api.o $(LDFLAGS) - - clean: - -rm $(KMC_MAIN_DIR)/*.o diff --git a/debian/patches/remove-all-zlib-libz2-include-statements b/debian/patches/remove-all-zlib-libz2-include-statements deleted file mode 100644 index 019c8b3..0000000 --- a/debian/patches/remove-all-zlib-libz2-include-statements +++ /dev/null @@ -1,15 +0,0 @@ -Index: b/kmer_counter/fastq_reader.h -=================================================================== ---- a/kmer_counter/fastq_reader.h -+++ b/kmer_counter/fastq_reader.h -@@ -16,8 +16,8 @@ - #include <stdio.h> - #include <iostream> - --#include "libs/zlib.h" --#include "libs/bzlib.h" -+#include "zlib.h" -+#include "bzlib.h" - - - using namespace std; diff --git a/debian/patches/remove-call-to-asmlib-sub-in-kbsorter b/debian/patches/remove-call-to-asmlib-sub-in-kbsorter deleted file mode 100644 index b085a86..0000000 --- a/debian/patches/remove-call-to-asmlib-sub-in-kbsorter +++ /dev/null @@ -1,16 +0,0 @@ -Description: Removes a call to set memory cache. -asmlib subroutineIndex: kmc/kmer_counter/kb_sorter.h -=================================================================== -Index: b/kmer_counter/kb_sorter.h -=================================================================== ---- a/kmer_counter/kb_sorter.h -+++ b/kmer_counter/kb_sorter.h -@@ -247,8 +247,6 @@ template <typename KMER_T, unsigned SIZE - uint64 tmp_n_rec; - CMemDiskFile *file; - -- SetMemcpyCacheLimit(8); -- - // Process bins - while (!bq->completed()) - { diff --git a/debian/patches/remove-embedded-libraries-from-makefile b/debian/patches/remove-embedded-libraries-from-makefile deleted file mode 100644 index e39ec14..0000000 --- a/debian/patches/remove-embedded-libraries-from-makefile +++ /dev/null @@ -1,26 +0,0 @@ -Description: Removes the calls to the distributed -libraries -=================================================================== -Index: b/makefile -=================================================================== ---- a/makefile -+++ b/makefile -@@ -9,15 +9,15 @@ KMC_API_DIR = kmc_api - KMC_DUMP_DIR = kmc_dump - - CC = g++ --CFLAGS = -Wall -O3 -m64 -static -fopenmp -std=c++11 -I $(BOOST_H) --CLINK = -lm -static -fopenmp -O3 -std=c++11 -+CFLAGS = -Wall -O3 -m64 -fopenmp -std=c++11 -I $(BOOST_H) -+CLINK = -lm -fopenmp -O3 -std=c++11 - - .cpp.o: - $(CC) $(CFLAGS) $(CPPFLAGS) -c $< -o $@ - - kmc: $(KMC_MAIN_DIR)/kmer_counter.o $(KMC_MAIN_DIR)/mmer.o $(KMC_MAIN_DIR)/mem_disk_file.o $(KMC_MAIN_DIR)/rev_byte.o $(KMC_MAIN_DIR)/fastq_reader.o $(KMC_MAIN_DIR)/timer.o $(KMC_MAIN_DIR)/radix.o $(KMC_MAIN_DIR)/kb_completer.o $(KMC_MAIN_DIR)/kb_storer.o $(KMC_MAIN_DIR)/kmer.o - -mkdir -p $(KMC_BIN_DIR) -- $(CC) $(CPPFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $(KMC_MAIN_DIR)/kmer_counter.o $(KMC_MAIN_DIR)/mem_disk_file.o $(KMC_MAIN_DIR)/rev_byte.o $(KMC_MAIN_DIR)/mmer.o $(KMC_MAIN_DIR)/fastq_reader.o $(KMC_MAIN_DIR)/timer.o $(KMC_MAIN_DIR)/radix.o $(KMC_MAIN_DIR)/kb_completer.o $(KMC_MAIN_DIR)/kb_storer.o $(KMC_MAIN_DIR)/kmer.o $(KMC_MAIN_DIR)/libs/alibelf64.a $(KMC_MAIN_DIR)/libs/libz.a $(KMC_MAIN_DIR)/libs/libbz2.a $(BOOST_LIB)/libboost_thread.a $(BOOST_LIB)/libboost_filesystem.a $(BOOST_LIB [...] -+ $(CC) $(CPPFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $(KMC_MAIN_DIR)/kmer_counter.o $(KMC_MAIN_DIR)/mem_disk_file.o $(KMC_MAIN_DIR)/rev_byte.o $(KMC_MAIN_DIR)/mmer.o $(KMC_MAIN_DIR)/fastq_reader.o $(KMC_MAIN_DIR)/timer.o $(KMC_MAIN_DIR)/radix.o $(KMC_MAIN_DIR)/kb_completer.o $(KMC_MAIN_DIR)/kb_storer.o $(KMC_MAIN_DIR)/kmer.o $(BOOST_LIB)/libboost_thread.a $(BOOST_LIB)/libboost_filesystem.a $(BOOST_LIB)/libboost_system.a $(LDFLAGS) -lz -lbz2 - - kmc_dump: $(KMC_DUMP_DIR)/nc_utils.o $(KMC_API_DIR)/mmer.o $(KMC_DUMP_DIR)/kmc_dump.o $(KMC_API_DIR)/kmc_file.o $(KMC_API_DIR)/kmer_api.o - -mkdir -p $(KMC_BIN_DIR) diff --git a/debian/patches/remove-gz-and-bz-flags-from-compilation b/debian/patches/remove-gz-and-bz-flags-from-compilation deleted file mode 100644 index 86df646..0000000 --- a/debian/patches/remove-gz-and-bz-flags-from-compilation +++ /dev/null @@ -1,13 +0,0 @@ -Description: Removing -lz and -lbz2 from compilation command.Index: kmc/makefile -=================================================================== ---- kmc.orig/makefile -+++ kmc/makefile -@@ -17,7 +17,7 @@ CLINK = -lm -static -fopenmp -O3 -std=c+ - - kmc: $(KMC_MAIN_DIR)/kmer_counter.o $(KMC_MAIN_DIR)/mmer.o $(KMC_MAIN_DIR)/mem_disk_file.o $(KMC_MAIN_DIR)/rev_byte.o $(KMC_MAIN_DIR)/fastq_reader.o $(KMC_MAIN_DIR)/timer.o $(KMC_MAIN_DIR)/radix.o $(KMC_MAIN_DIR)/kb_completer.o $(KMC_MAIN_DIR)/kb_storer.o $(KMC_MAIN_DIR)/kmer.o - -mkdir -p $(KMC_BIN_DIR) -- $(CC) $(CPPFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $(KMC_MAIN_DIR)/kmer_counter.o $(KMC_MAIN_DIR)/mem_disk_file.o $(KMC_MAIN_DIR)/rev_byte.o $(KMC_MAIN_DIR)/mmer.o $(KMC_MAIN_DIR)/fastq_reader.o $(KMC_MAIN_DIR)/timer.o $(KMC_MAIN_DIR)/radix.o $(KMC_MAIN_DIR)/kb_completer.o $(KMC_MAIN_DIR)/kb_storer.o $(KMC_MAIN_DIR)/kmer.o $(BOOST_LIB)/libboost_thread.a $(BOOST_LIB)/libboost_filesystem.a $(BOOST_LIB)/libboost_system.a $(LDFLAGS) -lz -lbz2 -+ $(CC) $(CPPFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $(KMC_MAIN_DIR)/kmer_counter.o $(KMC_MAIN_DIR)/mem_disk_file.o $(KMC_MAIN_DIR)/rev_byte.o $(KMC_MAIN_DIR)/mmer.o $(KMC_MAIN_DIR)/fastq_reader.o $(KMC_MAIN_DIR)/timer.o $(KMC_MAIN_DIR)/radix.o $(KMC_MAIN_DIR)/kb_completer.o $(KMC_MAIN_DIR)/kb_storer.o $(KMC_MAIN_DIR)/kmer.o $(BOOST_LIB)/libboost_thread.a $(BOOST_LIB)/libboost_filesystem.a $(BOOST_LIB)/libboost_system.a $(LDFLAGS) - - kmc_dump: $(KMC_DUMP_DIR)/nc_utils.o $(KMC_API_DIR)/mmer.o $(KMC_DUMP_DIR)/kmc_dump.o $(KMC_API_DIR)/kmc_file.o $(KMC_API_DIR)/kmer_api.o - -mkdir -p $(KMC_BIN_DIR) diff --git a/debian/patches/remove-references-to-asmlib b/debian/patches/remove-references-to-asmlib deleted file mode 100644 index 9ae0eac..0000000 --- a/debian/patches/remove-references-to-asmlib +++ /dev/null @@ -1,44 +0,0 @@ -Description: Removes all - include "libs/asmlib.h". -This is a customised subroutine optimisaiton library -that gives KMC a speed performance increase of ~0.66% -when compared ot the native library. -A decision was made togehter with upstream to remove -this dependency for the Debian package. - - -Index: b/kmer_counter/kmc.h -=================================================================== ---- a/kmer_counter/kmc.h -+++ b/kmer_counter/kmc.h -@@ -29,7 +29,6 @@ - #include "kb_storer.h" - #include "s_mapper.h" - #include "splitter.h" --#include "libs/asmlib.h" - #include <boost/filesystem.hpp> - - #ifdef DEVELOP_MODE -Index: b/kmer_counter/mem_disk_file.cpp -=================================================================== ---- a/kmer_counter/mem_disk_file.cpp -+++ b/kmer_counter/mem_disk_file.cpp -@@ -10,7 +10,6 @@ - */ - - #include "mem_disk_file.h" --#include "libs/asmlib.h" - - //---------------------------------------------------------------------------------- - // Constructor -Index: b/kmer_counter/radix.h -=================================================================== ---- a/kmer_counter/radix.h -+++ b/kmer_counter/radix.h -@@ -16,7 +16,6 @@ - #include <iostream> - #include <omp.h> - #include <algorithm> --#include "libs/asmlib.h" - #include "defs.h" - #include "queues.h" - #include <boost/static_assert.hpp> diff --git a/debian/patches/remove-use-of-asmlib-subroutines.patch b/debian/patches/remove-use-of-asmlib-subroutines.patch deleted file mode 100644 index 22a89fa..0000000 --- a/debian/patches/remove-use-of-asmlib-subroutines.patch +++ /dev/null @@ -1,141 +0,0 @@ -Description: Removes all usage of the "A_mem" subroutines. -The A_mem type of calls are defined in the asmlib library. - -Index: b/kmer_counter/defs.h -=================================================================== ---- a/kmer_counter/defs.h -+++ b/kmer_counter/defs.h -@@ -73,8 +73,6 @@ typedef float count_t; - #define KMER_WORDS ((MAX_K + 31) / 32) - - #ifdef _DEBUG --#define A_memcpy memcpy --#define A_memset memset - #endif - - -Index: b/kmer_counter/kb_sorter.h -=================================================================== ---- a/kmer_counter/kb_sorter.h -+++ b/kmer_counter/kb_sorter.h -@@ -406,7 +406,7 @@ template <unsigned SIZE> void CKmerBinSo - template <unsigned SIZE> void CKmerBinSorter_Impl<CKmer<SIZE>, SIZE>::FromChildThread(CKmerBinSorter<CKmer<SIZE>, SIZE>& ptr, CKmer<SIZE>* thread_buffer, uint64 size) - { - lock_guard<mutex> lcx(ptr.expander_mtx); -- A_memcpy(ptr.buffer_input + ptr.input_pos, thread_buffer, size * sizeof(CKmer<SIZE>)); -+ memcpy(ptr.buffer_input + ptr.input_pos, thread_buffer, size * sizeof(CKmer<SIZE>)); - ptr.input_pos += size; - } - -@@ -1359,4 +1359,4 @@ template <typename KMER_T, unsigned SIZE - - #endif - --// ***** EOF -\ No newline at end of file -+// ***** EOF -Index: b/kmer_counter/kb_storer.cpp -=================================================================== ---- a/kmer_counter/kb_storer.cpp -+++ b/kmer_counter/kb_storer.cpp -@@ -156,7 +156,7 @@ void CKmerBinStorer::PutBinToTmpFile(uin - { - buf = get<0>(*p); - size = get<1>(*p); -- A_memcpy(tmp_buff + tmp_buff_pos, buf, size); -+ memcpy(tmp_buff + tmp_buff_pos, buf, size); - tmp_buff_pos += size; - pmm_bins->free(buf); - } -Index: b/kmer_counter/mem_disk_file.cpp -=================================================================== ---- a/kmer_counter/mem_disk_file.cpp -+++ b/kmer_counter/mem_disk_file.cpp -@@ -78,7 +78,7 @@ size_t CMemDiskFile::Read(uchar * ptr, s - uint64 pos = 0; - for(auto& p : container) - { -- A_memcpy(ptr + pos, p.first, p.second); -+ memcpy(ptr + pos, p.first, p.second); - pos += p.second; - delete[] p.first; - } -@@ -97,7 +97,7 @@ size_t CMemDiskFile::Write(const uchar * - if(memory_mode) - { - uchar *buf = new uchar[size * count]; -- A_memcpy(buf, ptr, size * count); -+ memcpy(buf, ptr, size * count); - container.push_back(make_pair(buf, size * count)); - return size * count; - } -Index: b/kmer_counter/radix.cpp -=================================================================== ---- a/kmer_counter/radix.cpp -+++ b/kmer_counter/radix.cpp -@@ -72,7 +72,7 @@ void RadixOMP_uint8(uint32 *SourcePtr, u - - ++privateByteCounter[byteValue]; - } -- A_memcpy(&ByteCounter[myID][0], privateByteCounter, sizeof(privateByteCounter)); -+ memcpy(&ByteCounter[myID][0], privateByteCounter, sizeof(privateByteCounter)); - - #pragma omp barrier - -@@ -104,7 +104,7 @@ void RadixOMP_uint8(uint32 *SourcePtr, u - for (private_i = 0; private_i < 256; private_i++) - ByteCounter[myID][private_i] += globalHisto[private_i]; - -- A_memcpy(privateByteCounter, &ByteCounter[myID][0], sizeof(privateByteCounter)); -+ memcpy(privateByteCounter, &ByteCounter[myID][0], sizeof(privateByteCounter)); - - #pragma omp for schedule(static) - for(i = data_offset; i < SourceSize_in_bytes; i = i + rec_size) -@@ -199,7 +199,7 @@ template<typename COUNTER_TYPE, typename - byteValue = *(reinterpret_cast<const uint8_t*>(&tempSource[i]) + ByteIndex); - ++privateByteCounter[byteValue]; - } -- A_memcpy(&ByteCounter[myID][0], privateByteCounter, sizeof(privateByteCounter)); -+ memcpy(&ByteCounter[myID][0], privateByteCounter, sizeof(privateByteCounter)); - - #pragma omp barrier - -@@ -230,7 +230,7 @@ template<typename COUNTER_TYPE, typename - for (private_i = 0; private_i < 256; private_i++) - ByteCounter[myID][private_i] += globalHisto[private_i]; - -- A_memcpy(privateByteCounter, &ByteCounter[myID][0], sizeof(privateByteCounter)); -+ memcpy(privateByteCounter, &ByteCounter[myID][0], sizeof(privateByteCounter)); - - - #pragma omp for schedule(static) -@@ -245,7 +245,7 @@ template<typename COUNTER_TYPE, typename - privateByteCounter[byteValue]++; - - if(index_x == (BUFFER_WIDTH -1)) -- A_memcpy ( &tempDest[privateByteCounter[byteValue] - (BUFFER_WIDTH)], &Buffer[byteValue * BUFFER_WIDTH], BUFFER_WIDTH *sizeof(uint64) ); -+ memcpy ( &tempDest[privateByteCounter[byteValue] - (BUFFER_WIDTH)], &Buffer[byteValue * BUFFER_WIDTH], BUFFER_WIDTH *sizeof(uint64) ); - } //end_for - - INT_TYPE elemInBuffer; -@@ -265,7 +265,7 @@ template<typename COUNTER_TYPE, typename - elemInBuffer = index_stop - index_start; - - if(elemInBuffer != 0) -- A_memcpy ( &tempDest[privateByteCounter[private_i] - elemInBuffer], &Buffer[private_i * BUFFER_WIDTH + (privateByteCounter[private_i] - elemInBuffer)%BUFFER_WIDTH], (elemInBuffer)*sizeof(uint64) ); -+ memcpy ( &tempDest[privateByteCounter[private_i] - elemInBuffer], &Buffer[private_i * BUFFER_WIDTH + (privateByteCounter[private_i] - elemInBuffer)%BUFFER_WIDTH], (elemInBuffer)*sizeof(uint64) ); - - } - #pragma omp barrier -Index: b/kmer_counter/kmc.h -=================================================================== ---- a/kmer_counter/kmc.h -+++ b/kmer_counter/kmc.h -@@ -164,7 +164,6 @@ template <typename KMER_T, unsigned SIZE - - initialized = true; - -- SetMemcpyCacheLimit(8); // Sets the asmlib's memcpy function to make copy without use of cache memory - } - - //---------------------------------------------------------------------------------- diff --git a/debian/patches/removing-static-option-in-makefile b/debian/patches/removing-static-option-in-makefile deleted file mode 100644 index 4415469..0000000 --- a/debian/patches/removing-static-option-in-makefile +++ /dev/null @@ -1 +0,0 @@ -Description: Removes the static compilation option \ No newline at end of file diff --git a/debian/patches/series b/debian/patches/series deleted file mode 100644 index b081585..0000000 --- a/debian/patches/series +++ /dev/null @@ -1,6 +0,0 @@ -debian-dependent-makefile.patch -remove-references-to-asmlib -remove-use-of-asmlib-subroutines.patch -change-kmc-zlib-and-libz2-to-deb-zlib-and-libbz2 -remove-call-to-asmlib-sub-in-kbsorter -remove-embedded-libraries-from-makefile diff --git a/debian/rules b/debian/rules deleted file mode 100755 index ad78fa4..0000000 --- a/debian/rules +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/make -f - -export DH_VERBOSE := 1 -DEBVERS := $(shell dpkg-parsechangelog | sed -n -e 's/^Version: //p') -VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[~-].*//') -OVERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[+].*//') - - -mandir := $(CURDIR)/debian/man -debfolder := $(CURDIR)/debian - -%: - dh $@ - -override_dh_install: - dh_install - -override_dh_installman: - mkdir -p $(mandir) - $(debfolder)/usage_to_man - dh_installman -- - -get-orig-source: - uscan --verbose --force-download --repack --compression gz --destdir=.. - mv ../kmc_$(OVERSION).orig.tar.gz ../kmc_$(VERSION).orig.tar.gz diff --git a/debian/source/format b/debian/source/format deleted file mode 100644 index 46ebe02..0000000 --- a/debian/source/format +++ /dev/null @@ -1 +0,0 @@ -3.0 (quilt) \ No newline at end of file diff --git a/debian/upstream/metadata b/debian/upstream/metadata deleted file mode 100644 index d8b5812..0000000 --- a/debian/upstream/metadata +++ /dev/null @@ -1,12 +0,0 @@ -Reference: - Author: - Title: - Journal: - Year: - Volume: - Number: - Pages: - DOI: - PMID: - URL: - eprint: diff --git a/debian/usage_to_man b/debian/usage_to_man deleted file mode 100755 index e69a4bb..0000000 --- a/debian/usage_to_man +++ /dev/null @@ -1,140 +0,0 @@ -#!/usr/bin/perl -use strict; -use warnings; -use Data::Dumper; - -#Converts Fastaq python scripts usage into man pages. -#The man pages are placed in the man folder of the main Fastaq directory - -createManPages(); - -sub createManPages { - - my $source= 'bin'; - my $destination= '.'; - my $app_name = 'KMC'; - - - unless ( -d $destination ) { - system(mkdir $destination); - } - - my @files; - - push(@files,`ls $source/kmc*`); - - if ( scalar @files > 0 ) { - - print "Creating manpages\n"; - for my $file ( @files ) { - $file =~ s/\n$//; - - my $filename = $file; - $filename =~ s/$source\///; - - my $uc_filename = uc($filename); - my $man_file = $filename; - - $man_file = $destination . '/' . $man_file . '.1'; - - my $kmc_short_description = 'Count kmers in genomic sequences'; - my $kmc_long_description = 'KMC—K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.'; - - - my $cmd = "help2man -N -m $filename -n $filename --no-discard-stderr $file | sed 's/usage://gi'"; - my @output; - push(@output, `$cmd`); - - for my $line (@output) { - $line =~ s/\n$//; - - } - my $ss_param_seen = 0; - my $ss_param_seen2 = 1; - my $ip_tag_seen = 0; - my @lines_not_to_print; - my @lines_to_print; - - for (my $i = 0; $i < scalar @output; $i++) { - - - my $output_line = $output[$i]; - - $output_line =~ s/^(\.TH\s)([a-zA-Z0-9-]+)(\s.*)/$1 $filename $3/; - $output_line =~ s/^(K\-Mer \\- )(kmc)/$2 - $kmc_short_description/; - if ($output_line =~ m/^K\\-Mer Counter/) { - $output_line = $kmc_long_description; - } - - if ($output_line =~ m/^\.SS \"Parameters\:\"/ && ! $ss_param_seen) { - push(@lines_not_to_print, $i); - push(@lines_not_to_print, $i + 1); - push(@lines_not_to_print, $i + 2); - push(@lines_not_to_print, $i + 3); - - $ss_param_seen = 1; - $ss_param_seen2 = 0; - - } - elsif ($output_line =~ m/^\.IP/ && ! $ip_tag_seen) { - $output_line = '.SH SYNOPSIS'; - if ($output[$i + 2] =~ /^kmc/) { - $output[$i +2] = ".PP\n" . $output[$i + 2]; - } - $ip_tag_seen = 1; - } - elsif ($output_line =~ m/^\.SS ""/) { - push(@lines_not_to_print, $i); - push(@lines_not_to_print, $i + 1); - push(@lines_not_to_print, $i + 2); - push(@lines_not_to_print, $i + 3); - } - elsif ($output_line =~ m/^Example:/) { - $output_line = '.SH EXAMPLES'; - $output[$i + 2] = ".PP\n" . $output[$i + 2]; - - } - elsif ($output_line =~ m/^\.SS \"Parameters\:\"/ && $ss_param_seen && ! $ss_param_seen2) { - last; - - } - - if ( ! grep( /^$i$/, @lines_not_to_print ) ){ - #print "$output_line\n"; - push(@lines_to_print, $output_line); - } - - - } - print Dumper(\@lines_not_to_print); - open (my $man_fh, ">", $man_file); - for my $line(@lines_to_print) { - print $man_fh "$line\n"; - } - close($man_fh); - print "Manpage creation complete\n"; - } - } -} - -sub writeAuthorAndCopyright { - - my ($man_fh,$filename) = @_; - - my $author_blurb = <<END_OF_AUTHOR_BLURB; -.SH "AUTHOR" -.sp -$filename was originally written by Martin Hunt (mh12\@sanger.ac.uk) -END_OF_AUTHOR_BLURB - - print $man_fh "$author_blurb\n"; - - my $copyright_blurb = <<'END_OF_C_BLURB'; -.SH "COPYING" -.sp -Wellcome Trust Sanger Institute Copyright \(co 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version\&. -END_OF_C_BLURB - - print $man_fh "$copyright_blurb\n"; - -} diff --git a/debian/watch b/debian/watch deleted file mode 100644 index bf30b45..0000000 --- a/debian/watch +++ /dev/null @@ -1,5 +0,0 @@ -version=3 - -opts=dversionmangle=s/[~\+]dfsg[0-9]*// \ - https://github.com/js21/kmc/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) - -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/kmc.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
