[med-svn] [kmc] 05/15: patches
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Mon Aug 24 21:25:07 UTC 2015
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository kmc.
commit 13afcd8ed55a55223fe883bcb125d5d67d28f61c
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Mon Aug 24 19:20:04 2015 +0000
patches
---
...-libz2-include-statements-to-native-debian-libs | 40 ++---
...hange-kmc-zlib-and-libz2-to-deb-zlib-and-libbz2 | 20 +--
.../remove-all-zlib-libz2-include-statements | 20 +--
.../patches/remove-call-to-asmlib-sub-in-kbsorter | 16 +-
debian/patches/remove-references-to-asmlib | 42 ++---
.../patches/remove-use-of-asmlib-subroutines.patch | 198 ++++++++++-----------
debian/patches/series | 10 +-
7 files changed, 172 insertions(+), 174 deletions(-)
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
index 0355fbe..212aa14 100644
--- 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
@@ -3,28 +3,28 @@ 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;
+ #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;
+ #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
index 80091d2..af9f4c8 100644
--- 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
@@ -6,13 +6,13 @@ 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;
+ #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-all-zlib-libz2-include-statements b/debian/patches/remove-all-zlib-libz2-include-statements
index 019c8b3..c4da373 100644
--- a/debian/patches/remove-all-zlib-libz2-include-statements
+++ b/debian/patches/remove-all-zlib-libz2-include-statements
@@ -3,13 +3,13 @@ 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;
+ #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
index b085a86..84fd718 100644
--- a/debian/patches/remove-call-to-asmlib-sub-in-kbsorter
+++ b/debian/patches/remove-call-to-asmlib-sub-in-kbsorter
@@ -6,11 +6,11 @@ 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())
- {
+ uint64 tmp_n_rec;
+ CMemDiskFile *file;
+
+- SetMemcpyCacheLimit(8);
+-
+ // Process bins
+ while (!bq->completed())
+ {
diff --git a/debian/patches/remove-references-to-asmlib b/debian/patches/remove-references-to-asmlib
index 9ae0eac..ee1ec9a 100644
--- a/debian/patches/remove-references-to-asmlib
+++ b/debian/patches/remove-references-to-asmlib
@@ -11,34 +11,34 @@ 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
+ #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
+ */
+
+ #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>
+ #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
index 22a89fa..79a5bfb 100644
--- a/debian/patches/remove-use-of-asmlib-subroutines.patch
+++ b/debian/patches/remove-use-of-asmlib-subroutines.patch
@@ -6,136 +6,136 @@ 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
-
-
+ #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;
- }
-
+ 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
-
+
+ #endif
+
-// ***** EOF
\ No newline at end of file
-+// ***** EOF
++// ***** 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);
- }
+ {
+ 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;
- }
+ 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;
- }
+ 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
-
+
+ ++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)
+ 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
-
+ 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)
+ 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;
+ 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
+ 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
- }
-
- //----------------------------------------------------------------------------------
+
+ initialized = true;
+
+- SetMemcpyCacheLimit(8); // Sets the asmlib's memcpy function to make copy without use of cache memory
+ }
+
+ //----------------------------------------------------------------------------------
diff --git a/debian/patches/series b/debian/patches/series
index b081585..2a1d604 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,4 @@
-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
+disable-asmlib
+use-shared-libs
+allow-dry-clean
+hardening
--
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