[med-svn] [kmc] 01/02: Imported Upstream version 2.0+dfsg-1
Jorge Soares
jssoares-guest at moszumanska.debian.org
Tue Nov 18 12:53:48 UTC 2014
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 <j.s.soares at gmail.com>
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 <j.s.soares at gmail.com> 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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
- Jorge Soares <j.s.soares at gmail.com>
-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)
-
--
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