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debian/changelog
View file @ 1cf350ab
kmc (2.3+dfsg-6) unstable; urgency=medium
* Drop unneeded get-orig-source target
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
* Drop unnecessary Testsuite: autopkgtest
* Do not parse d/changelog
* Fix spelling
-- Andreas Tille <tille@debian.org> Wed, 11 Jul 2018 21:35:03 +0200
kmc (2.3+dfsg-5) unstable; urgency=medium
* Add missing include to header, fixes FTBFS.
......
debian/control
View file @ 1cf350ab
......@@ -6,17 +6,16 @@ Uploaders: Andreas Tille <tille@debian.org>,
Kevin Murray <spam@kdmurray.id.au>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
Build-Depends: debhelper (>= 11~),
dh-exec,
zlib1g-dev,
libbz2-dev,
help2man,
asciidoctor,
d-shlibs
Standards-Version: 3.9.7
Testsuite: autopkgtest
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/kmc.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/kmc.git
Standards-Version: 4.1.5
Vcs-Browser: https://salsa.debian.org/med-team/kmc
Vcs-Git: https://salsa.debian.org/med-team/kmc.git
Homepage: http://sun.aei.polsl.pl/kmc
Package: kmc
......@@ -47,8 +46,8 @@ Description: count kmers in genomic sequences
order of the size of input data (usually it is smaller).
Package: libkmc-dev
Section: libdevel
Architecture: any
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends}
Description: library to access KMC k-mer count files
......
debian/patches/0006-Fix-wildcard-to-define-libkmc-objects.patch deleted 100644 → 0
View file @ 55b0e172
From: Kevin Murray <spam@kdmurray.id.au>
Date: Fri, 2 Oct 2015 09:58:41 +1000
Subject: Fix wildcard to define libkmc objects
---
makefile | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/makefile b/makefile
index bc2ed0f..ff7357d 100644
--- a/makefile
+++ b/makefile
@@ -23,14 +23,15 @@ $(KMC_MAIN_DIR)/kb_completer.o \
$(KMC_MAIN_DIR)/kb_storer.o \
$(KMC_MAIN_DIR)/kmer.o
-KMC_DUMP_OBJS = \
-$(KMC_DUMP_DIR)/nc_utils.o \
+KMC_LIB_OBJS = \
$(KMC_API_DIR)/mmer.o \
-$(KMC_DUMP_DIR)/kmc_dump.o \
$(KMC_API_DIR)/kmc_file.o \
$(KMC_API_DIR)/kmer_api.o
-KMC_LIB_OBJS = $(wildcard $(KMC_API_DIR)/*.o)
+KMC_DUMP_OBJS = \
+$(KMC_DUMP_DIR)/nc_utils.o \
+$(KMC_DUMP_DIR)/kmc_dump.o \
+$(KMC_LIB_OBJS)
ifeq ($(DISABLE_ASMLIB),true)
CFLAGS += -DDISABLE_ASMLIB
debian/patches/allow-dry-clean deleted 100644 → 0
View file @ 55b0e172
From: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Date: Thu, 1 Oct 2015 16:13:54 +1000
Subject: allow-dry-clean
---
makefile | 9 +++------
1 file changed, 3 insertions(+), 6 deletions(-)
diff --git a/makefile b/makefile
index 0706eb3..71dd3b2 100644
--- a/makefile
+++ b/makefile
@@ -52,9 +49,9 @@ kmc_dump: $(KMC_DUMP_OBJS)
-mkdir -p $(KMC_BIN_DIR)
$(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
clean:
- -rm $(KMC_MAIN_DIR)/*.o
- -rm $(KMC_API_DIR)/*.o
- -rm $(KMC_DUMP_DIR)/*.o
+ -rm -f $(KMC_MAIN_DIR)/*.o
+ -rm -f $(KMC_API_DIR)/*.o
+ -rm -f $(KMC_DUMP_DIR)/*.o
-rm -rf bin
all: kmc kmc_dump
debian/patches/spelling
View file @ 1cf350ab
......@@ -3,7 +3,7 @@ Author: Sascha Steinbiss <sascha@steinbiss.name>
Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
--- a/kmc_tools/config.h
+++ b/kmc_tools/config.h
@@ -243,7 +243,7 @@
@@ -243,11 +243,11 @@ public:
std::cout << " sort - sorts k-mers from database generated by KMC2.x\n";
std::cout << " reduce - exclude too rare and too frequent k-mers\n";
std::cout << " compact - remove counters (store only k-mers)\n";
......@@ -12,7 +12,21 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
std::cout << " dump - dump k-mers and counters to text file\n";
std::cout << " more complex operations:\n";
std::cout << " complex - complex operations with a number of input databases\n";
@@ -332,7 +332,7 @@
- std::cout << " other operatations:\n";
+ std::cout << " other operations:\n";
std::cout << " filter - filter out reads with too small number of k-mers\n";
std::cout << " global parameters:\n";
std::cout << " -t<value> - total number of threads (default: no. of CPU cores)\n";
@@ -301,7 +301,7 @@ public:
void Display() const override
{
Display2ArgGeneral();
- std::cout << "The output database will contains only k-mers that are present in first input set and have counters higher than apropriate k - mers in second set. For each k - mer the counter is equal to difference between counter in first set and counter in second set.";
+ std::cout << "The output database will contains only k-mers that are present in first input set and have counters higher than appropriate k - mers in second set. For each k - mer the counter is equal to difference between counter in first set and counter in second set.";
std::cout << "Example:\n";
std::cout << "kmc -k28 file1.fastq kmers1 tmp\n";
std::cout << "kmc -k28 file2.fastq kmers2 tmp\n";
@@ -332,7 +332,7 @@ public:
{}
void Display() const override
{
......@@ -21,7 +35,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
std::cout << "kmc_tools complex <operations_definition_file>\n";
std::cout << " operations_definition_file - path to file which define input sets and operations. It is text file with following syntax:\n";
std::cout << " __________________________________________________________________ \n";
@@ -355,7 +355,7 @@
@@ -355,7 +355,7 @@ public:
std::cout << "out_db_path - path to output database\n";
std::cout << "ref_input - one of input1, input2, ..., inputN\n";
std::cout << "oper - one of {*,-,~,+}, which refers to {intersect, kmers_subtract, counters_subtract, union}\n";
......@@ -30,7 +44,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
std::cout << "output_params are:\n";
std::cout << " -ci<value> - exclude k-mers occurring less than <value> times \n";
std::cout << " -cx<value> - exclude k-mers occurring more of than <value> times\n";
@@ -547,4 +547,4 @@
@@ -547,4 +547,4 @@ public:
#endif
......@@ -39,7 +53,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
+// ***** EOF
--- a/kmer_counter/bkb_sorter.h
+++ b/kmer_counter/bkb_sorter.h
@@ -367,7 +367,7 @@
@@ -367,7 +367,7 @@ template<unsigned SIZE> void CBigKmerBin
}
//----------------------------------------------------------------------------------
......@@ -50,7 +64,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
uint32 kxmer_offset = (ptr.kmer_len + ptr.max_x - offset) * 2;
--- a/kmer_counter/kb_sorter.h
+++ b/kmer_counter/kb_sorter.h
@@ -830,7 +830,7 @@
@@ -830,7 +830,7 @@ template <typename KMER_T, unsigned SIZE
}
//----------------------------------------------------------------------------------
......@@ -61,7 +75,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
uint32 kxmer_offset = (ptr.kmer_len + ptr.max_x - offset) * 2;
--- a/kmer_counter/s_mapper.h
+++ b/kmer_counter/s_mapper.h
@@ -30,12 +30,12 @@
@@ -30,12 +30,12 @@ class CSignatureMapper
class Comp
{
......@@ -79,7 +93,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
--- a/kmc_tools/kmc1_db_writer.h
+++ b/kmc_tools/kmc1_db_writer.h
@@ -37,7 +37,7 @@
@@ -37,7 +37,7 @@ public:
{
if (fwrite(buf, 1, size, kmc_suf) != size)
{
......@@ -88,7 +102,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
delete[] buf;
@@ -78,9 +78,9 @@
@@ -78,9 +78,9 @@ private:
void store_pre_buf();
void send_suf_buf_to_queue();
......@@ -100,7 +114,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
template<typename T> void write_header_part(T data);
void calc_lut_prefix_len();
@@ -159,7 +159,7 @@
@@ -159,7 +159,7 @@ template <unsigned SIZE> CKMC1DbWriter<S
template<unsigned SIZE> bool CKMC1DbWriter<SIZE>::Process()
{
......@@ -109,7 +123,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
//Converts bundles to output buffers, sufix buffer is placed to another queue and write in separate thread (sufix_writer)
std::thread preparing_thread([this]{
@@ -201,7 +201,7 @@
@@ -201,7 +201,7 @@ template<unsigned SIZE> bool CKMC1DbWrit
preparing_thread.join();
suf_buf_writing_thread.join();
......@@ -118,7 +132,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
return true;
}
@@ -232,22 +232,22 @@
@@ -232,22 +232,22 @@ template <unsigned SIZE> template <typen
}
/*****************************************************************************************************************************/
......@@ -145,7 +159,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
{
uint32 max_prefix = (1 << 2 * lut_prefix_len);
while (current_prefix < max_prefix - 1)
@@ -284,12 +284,12 @@
@@ -284,12 +284,12 @@ template<unsigned SIZE> void CKMC1DbWrit
if (fwrite("KMCP", 1, 4, kmc_pre) != 4)
{
......@@ -160,7 +174,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
fclose(kmc_pre);
@@ -327,7 +327,7 @@
@@ -327,7 +327,7 @@ template<unsigned SIZE> void CKMC1DbWrit
{
if (fwrite(pre_buff, sizeof(uint64), pre_pos, kmc_pre) != pre_pos)
{
......@@ -171,7 +185,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
pre_pos = 0;
--- a/kmer_counter/radix.cpp
+++ b/kmer_counter/radix.cpp
@@ -143,7 +143,7 @@
@@ -143,7 +143,7 @@ void RadixSort_uint8(uint32 *&data_ptr,
Satish, N., Kim, C., Chhugani, J., Nguyen, A.D., Lee, V.W., Kim, D., Dubey, P. (2010).
Fast Sort on CPUs and GPUs. A Case for Bandwidth Oblivious SIMD Sort.
Proc. of the 2010 Int. Conf. on Management of data, pp. 351–362.
......@@ -182,7 +196,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
template<typename COUNTER_TYPE, typename INT_TYPE>
--- a/kmc_tools/kmc2_db_reader.h
+++ b/kmc_tools/kmc2_db_reader.h
@@ -869,7 +869,7 @@
@@ -869,7 +869,7 @@ template<unsigned SIZE> CKMC2DbReaderSor
my_fseek(kmc_pre, 4, SEEK_SET);
if (fread(LUTS, sizeof(uint64), lut_recs, kmc_pre) != lut_recs)
{
......@@ -191,7 +205,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
fclose(kmc_pre);
@@ -1005,7 +1005,7 @@
@@ -1005,7 +1005,7 @@ template<unsigned SIZE> CKMC2DbReaderSor
// my_fseek(kmc_suf, start, SEEK_SET);
// if (fread(buf, 1, size, kmc_suf) != size)
// {
......@@ -200,7 +214,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
// exit(1);
// }
//#ifdef ENABLE_LOGGER
@@ -1336,7 +1336,7 @@
@@ -1336,7 +1336,7 @@ template<unsigned SIZE> CKMC2DbReader<SI
db_reader_counters_only = std::make_unique<CKMC2DbReaderCountersOnly<SIZE>>(header, desc);
break;
default: //should never be here
......@@ -209,7 +223,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
}
@@ -1395,4 +1395,4 @@
@@ -1395,4 +1395,4 @@ template<unsigned SIZE> bool CKMC2DbRead
......@@ -218,7 +232,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
+#endif
--- a/kmc_tools/parameters_parser.cpp
+++ b/kmc_tools/parameters_parser.cpp
@@ -140,7 +140,7 @@
@@ -140,7 +140,7 @@ void CParametersParser::read_input_fastq
config.filtering_params.input_file_type = CFilteringParams::file_type::fastq;
break;
default:
......@@ -227,7 +241,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
break;
}
@@ -207,7 +207,7 @@
@@ -207,7 +207,7 @@ void CParametersParser::read_dump_params
}
else
{
......@@ -236,7 +250,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
}
++pos;
}
@@ -242,7 +242,7 @@
@@ -242,7 +242,7 @@ void CParametersParser::read_input_desc(
}
else
{
......@@ -245,7 +259,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
}
@@ -279,7 +279,7 @@
@@ -279,7 +279,7 @@ void CParametersParser::read_output_desc
}
else
{
......@@ -254,7 +268,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
}
@@ -355,7 +355,7 @@
@@ -355,7 +355,7 @@ void CParametersParser::Parse()
}
else
{
......@@ -263,7 +277,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
Usage();
exit(1);
}
@@ -533,4 +533,4 @@
@@ -533,4 +533,4 @@ void CParametersParser::SetThreads()
......@@ -272,7 +286,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
+// ***** EOF
--- a/kmc_tools/parameters_parser.h
+++ b/kmc_tools/parameters_parser.h
@@ -67,7 +67,7 @@
@@ -67,7 +67,7 @@ CExpressionNode<SIZE>* CParametersParser
expression_root = new CCountersSubtractionNode<SIZE>;
break;
default:
......@@ -281,7 +295,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
expression_root->AddLeftChild(left);
@@ -98,7 +98,7 @@
@@ -98,7 +98,7 @@ CExpressionNode<SIZE>* CParametersParser
}
else //should never be here
{
......@@ -290,7 +304,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
#ifdef ENABLE_DEBUG
std::cout << __FUNCTION__ << " line: " << __LINE__ << "\n";
#endif
@@ -108,4 +108,4 @@
@@ -108,4 +108,4 @@ CExpressionNode<SIZE>* CParametersParser
#endif
......@@ -299,7 +313,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
+// ***** EOF
--- a/kmc_tools/parser.cpp
+++ b/kmc_tools/parser.cpp
@@ -115,7 +115,7 @@
@@ -115,7 +115,7 @@ void CParser::parseInputLine(const std::
desc.cutoff_max = atoi(tmp.c_str() + 3);
continue;
}
......@@ -308,7 +322,7 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
exit(1);
}
@@ -160,7 +160,7 @@
@@ -160,7 +160,7 @@ void CParser::parseOtuputParamsLine()
config.output_desc.counter_max = atoi(tmp.c_str() + 3);
continue;
}
......
debian/rules
View file @ 1cf350ab
......@@ -2,13 +2,15 @@
export DH_VERBOSE := 1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
DATE := $(shell dpkg-parsechangelog -S Date)
include /usr/share/dpkg/default.mk
DATE := $(SOURCE_DATE_EPOCH)
mandir := $(CURDIR)/debian/man
debfolder := $(CURDIR)/debian
%:
dh $@ --parallel
dh $@
override_dh_install:
dh_install
......@@ -24,6 +26,3 @@ override_dh_installman:
asciidoctor -a docdate='' -b manpage $(debfolder)/man_src/*.adoc
cp $(debfolder)/man_src/*.? $(mandir)
dh_installman --
get-orig-source:
uscan --verbose --force-download --repack --compression gz --destdir=..