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debian/changelog
View file @ a26e7942
mash (2.1+dfsg-1) UNRELEASED; urgency=medium
* Team upload.
* Remove code copy of MurmurHash and use libmurmurhash-dev instead
Closes: #919778, #918566
-- Andreas Tille <tille@debian.org> Tue, 05 Feb 2019 15:58:23 +0100
mash (2.1-2) unstable; urgency=medium
* Adjust CXXFLAGS due to new dependency requirements.
......
debian/control
View file @ a26e7942
......@@ -10,7 +10,8 @@ Build-Depends: debhelper (>= 11),
zlib1g-dev,
python3-sphinx,
libjs-mathjax,
asciidoctor
asciidoctor,
libmurmurhash-dev
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/mash
Vcs-Git: https://salsa.debian.org/med-team/mash.git
......
debian/copyright
View file @ a26e7942
......@@ -2,6 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Mash
Upstream-Contact: Adam Phillippy <adam.phillippy@nih.gov>
Source: https://github.com/marbl/Mash
Files-Excluded: */MurmurHash3*
Files: *
Copyright: © 2015 Battelle National Biodefense Institute (BNBI)
......@@ -72,12 +73,6 @@ License: MIT
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Files: src/mash/MurmurHash3.*
Copyright: Austin Appleby
License: public-domain
The original C++ code was placed in the public domain by its author,
Austin Appleby.
Files: src/mash/bloom_filter.hpp
Copyright: (c) 2000 Arash Partow
License: CPL
......
debian/patches/series
View file @ a26e7942
......@@ -4,3 +4,4 @@ drop_memcpy_wrapper.patch
link_dynamically_against_capnp.patch
parallel.patch
capnp0_7.patch
use_debian_packaged_libmurmurhash.patch
debian/patches/use_debian_packaged_libmurmurhash.patch 0 → 100644
View file @ a26e7942
Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 05 Feb 2019 15:58:23 +0100
Description: use debian packaged libmurmurhash
--- a/Makefile.in
+++ b/Makefile.in
@@ -24,7 +24,6 @@ SOURCES=\
src/mash/HashPriorityQueue.cpp \
src/mash/HashSet.cpp \
src/mash/MinHashHeap.cpp \
- src/mash/MurmurHash3.cpp \
src/mash/mash.cpp \
src/mash/Sketch.cpp \
src/mash/sketchParameterSetup.cpp \
@@ -34,7 +33,7 @@ OBJECTS=$(SOURCES:.cpp=.o) src/mash/capn
all : mash libmash.a
mash : $(OBJECTS)
- $(CXX) $(CXXFLAGS) $(CPPFLAGS) -o mash $(OBJECTS) -lkj -lcapnp @mathlib@ -lstdc++ -lz -lm -lpthread $(LDFLAGS)
+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -o mash $(OBJECTS) -lkj -lcapnp @mathlib@ -lstdc++ -lz -lm -lpthread -lmurmurhash $(LDFLAGS)
libmash.a : $(OBJECTS)
ar -cr libmash.a $(OBJECTS)
--- a/src/mash/Sketch.cpp
+++ b/src/mash/Sketch.cpp
@@ -12,7 +12,7 @@
#include <fcntl.h>
#include <map>
#include "kseq.h"
-#include "MurmurHash3.h"
+#include <murmurhash.h>
#include <assert.h>
#include <queue>
#include <deque>
--- a/src/mash/hash.cpp
+++ b/src/mash/hash.cpp
@@ -5,7 +5,7 @@
// See the LICENSE.txt file included with this software for license information.
#include "hash.h"
-#include "MurmurHash3.h"
+#include <murmurhash.h>
hash_u getHash(const char * seq, int length, uint32_t seed, bool use64)
{
debian/watch
View file @ a26e7942
version=3
version=4
opts="compress=xz" \
https://github.com/marbl/Mash/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
https://github.com/marbl/Mash/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@
src/mash/MurmurHash3.cpp deleted 100644 → 0
View file @ 076de3b2
//-----------------------------------------------------------------------------
// MurmurHash3 was written by Austin Appleby, and is placed in the public
// domain. The author hereby disclaims copyright to this source code.
// Note - The x86 and x64 versions do _not_ produce the same results, as the
// algorithms are optimized for their respective platforms. You can still
// compile and run any of them on any platform, but your performance with the
// non-native version will be less than optimal.
#include "MurmurHash3.h"
//-----------------------------------------------------------------------------
// Platform-specific functions and macros
// Microsoft Visual Studio
#if defined(_MSC_VER)
#define FORCE_INLINE __forceinline
#include <stdlib.h>
#define ROTL32(x,y) _rotl(x,y)
#define ROTL64(x,y) _rotl64(x,y)
#define BIG_CONSTANT(x) (x)
// Other compilers
#else // defined(_MSC_VER)
#define FORCE_INLINE inline __attribute__((always_inline))
inline uint32_t rotl32 ( uint32_t x, int8_t r )
{
return (x << r) | (x >> (32 - r));
}
inline uint64_t rotl64 ( uint64_t x, int8_t r )
{
return (x << r) | (x >> (64 - r));
}
#define ROTL32(x,y) rotl32(x,y)
#define ROTL64(x,y) rotl64(x,y)
#define BIG_CONSTANT(x) (x##LLU)
#endif // !defined(_MSC_VER)
//-----------------------------------------------------------------------------
// Block read - if your platform needs to do endian-swapping or can only
// handle aligned reads, do the conversion here
FORCE_INLINE uint32_t getblock32 ( const uint32_t * p, int i )
{
return p[i];
}
FORCE_INLINE uint64_t getblock64 ( const uint64_t * p, int i )
{
return p[i];
}
//-----------------------------------------------------------------------------
// Finalization mix - force all bits of a hash block to avalanche
FORCE_INLINE uint32_t fmix32 ( uint32_t h )
{
h ^= h >> 16;
h *= 0x85ebca6b;
h ^= h >> 13;
h *= 0xc2b2ae35;
h ^= h >> 16;
return h;
}
//----------
FORCE_INLINE uint64_t fmix64 ( uint64_t k )
{
k ^= k >> 33;
k *= BIG_CONSTANT(0xff51afd7ed558ccd);
k ^= k >> 33;
k *= BIG_CONSTANT(0xc4ceb9fe1a85ec53);
k ^= k >> 33;
return k;
}
//-----------------------------------------------------------------------------
void MurmurHash3_x86_32 ( const void * key, int len,
uint32_t seed, void * out )
{
const uint8_t * data = (const uint8_t*)key;
const int nblocks = len / 4;
uint32_t h1 = seed;
const uint32_t c1 = 0xcc9e2d51;
const uint32_t c2 = 0x1b873593;
//----------
// body
const uint32_t * blocks = (const uint32_t *)(data + nblocks*4);
for(int i = -nblocks; i; i++)
{
uint32_t k1 = getblock32(blocks,i);
k1 *= c1;
k1 = ROTL32(k1,15);
k1 *= c2;
h1 ^= k1;
h1 = ROTL32(h1,13);
h1 = h1*5+0xe6546b64;
}
//----------
// tail
const uint8_t * tail = (const uint8_t*)(data + nblocks*4);
uint32_t k1 = 0;
switch(len & 3)
{
case 3: k1 ^= tail[2] << 16;
case 2: k1 ^= tail[1] << 8;
case 1: k1 ^= tail[0];
k1 *= c1; k1 = ROTL32(k1,15); k1 *= c2; h1 ^= k1;
};
//----------
// finalization
h1 ^= len;
h1 = fmix32(h1);
*(uint32_t*)out = h1;
}
//-----------------------------------------------------------------------------
void MurmurHash3_x86_128 ( const void * key, const int len,
uint32_t seed, void * out )
{
const uint8_t * data = (const uint8_t*)key;
const int nblocks = len / 16;
uint32_t h1 = seed;
uint32_t h2 = seed;
uint32_t h3 = seed;
uint32_t h4 = seed;
const uint32_t c1 = 0x239b961b;
const uint32_t c2 = 0xab0e9789;
const uint32_t c3 = 0x38b34ae5;
const uint32_t c4 = 0xa1e38b93;
//----------
// body
const uint32_t * blocks = (const uint32_t *)(data + nblocks*16);
for(int i = -nblocks; i; i++)
{
uint32_t k1 = getblock32(blocks,i*4+0);
uint32_t k2 = getblock32(blocks,i*4+1);
uint32_t k3 = getblock32(blocks,i*4+2);
uint32_t k4 = getblock32(blocks,i*4+3);
k1 *= c1; k1 = ROTL32(k1,15); k1 *= c2; h1 ^= k1;
h1 = ROTL32(h1,19); h1 += h2; h1 = h1*5+0x561ccd1b;
k2 *= c2; k2 = ROTL32(k2,16); k2 *= c3; h2 ^= k2;
h2 = ROTL32(h2,17); h2 += h3; h2 = h2*5+0x0bcaa747;
k3 *= c3; k3 = ROTL32(k3,17); k3 *= c4; h3 ^= k3;
h3 = ROTL32(h3,15); h3 += h4; h3 = h3*5+0x96cd1c35;
k4 *= c4; k4 = ROTL32(k4,18); k4 *= c1; h4 ^= k4;
h4 = ROTL32(h4,13); h4 += h1; h4 = h4*5+0x32ac3b17;
}
//----------
// tail
const uint8_t * tail = (const uint8_t*)(data + nblocks*16);
uint32_t k1 = 0;
uint32_t k2 = 0;
uint32_t k3 = 0;
uint32_t k4 = 0;
switch(len & 15)
{
case 15: k4 ^= tail[14] << 16;
case 14: k4 ^= tail[13] << 8;
case 13: k4 ^= tail[12] << 0;
k4 *= c4; k4 = ROTL32(k4,18); k4 *= c1; h4 ^= k4;
case 12: k3 ^= tail[11] << 24;
case 11: k3 ^= tail[10] << 16;
case 10: k3 ^= tail[ 9] << 8;
case 9: k3 ^= tail[ 8] << 0;
k3 *= c3; k3 = ROTL32(k3,17); k3 *= c4; h3 ^= k3;
case 8: k2 ^= tail[ 7] << 24;
case 7: k2 ^= tail[ 6] << 16;
case 6: k2 ^= tail[ 5] << 8;
case 5: k2 ^= tail[ 4] << 0;
k2 *= c2; k2 = ROTL32(k2,16); k2 *= c3; h2 ^= k2;
case 4: k1 ^= tail[ 3] << 24;
case 3: k1 ^= tail[ 2] << 16;
case 2: k1 ^= tail[ 1] << 8;
case 1: k1 ^= tail[ 0] << 0;
k1 *= c1; k1 = ROTL32(k1,15); k1 *= c2; h1 ^= k1;
};
//----------
// finalization
h1 ^= len; h2 ^= len; h3 ^= len; h4 ^= len;
h1 += h2; h1 += h3; h1 += h4;
h2 += h1; h3 += h1; h4 += h1;
h1 = fmix32(h1);
h2 = fmix32(h2);
h3 = fmix32(h3);
h4 = fmix32(h4);
h1 += h2; h1 += h3; h1 += h4;
h2 += h1; h3 += h1; h4 += h1;
((uint32_t*)out)[0] = h1;
((uint32_t*)out)[1] = h2;
((uint32_t*)out)[2] = h3;
((uint32_t*)out)[3] = h4;
}
//-----------------------------------------------------------------------------
void MurmurHash3_x64_128 ( const void * key, const int len,
const uint32_t seed, void * out )
{
const uint8_t * data = (const uint8_t*)key;
const int nblocks = len / 16;
uint64_t h1 = seed;
uint64_t h2 = seed;
const uint64_t c1 = BIG_CONSTANT(0x87c37b91114253d5);
const uint64_t c2 = BIG_CONSTANT(0x4cf5ad432745937f);
//----------
// body
const uint64_t * blocks = (const uint64_t *)(data);
for(int i = 0; i < nblocks; i++)
{
uint64_t k1 = getblock64(blocks,i*2+0);
uint64_t k2 = getblock64(blocks,i*2+1);
k1 *= c1; k1 = ROTL64(k1,31); k1 *= c2; h1 ^= k1;
h1 = ROTL64(h1,27); h1 += h2; h1 = h1*5+0x52dce729;
k2 *= c2; k2 = ROTL64(k2,33); k2 *= c1; h2 ^= k2;
h2 = ROTL64(h2,31); h2 += h1; h2 = h2*5+0x38495ab5;
}
//----------
// tail
const uint8_t * tail = (const uint8_t*)(data + nblocks*16);
uint64_t k1 = 0;
uint64_t k2 = 0;
switch(len & 15)
{
case 15: k2 ^= ((uint64_t)tail[14]) << 48;
case 14: k2 ^= ((uint64_t)tail[13]) << 40;
case 13: k2 ^= ((uint64_t)tail[12]) << 32;
case 12: k2 ^= ((uint64_t)tail[11]) << 24;
case 11: k2 ^= ((uint64_t)tail[10]) << 16;
case 10: k2 ^= ((uint64_t)tail[ 9]) << 8;
case 9: k2 ^= ((uint64_t)tail[ 8]) << 0;
k2 *= c2; k2 = ROTL64(k2,33); k2 *= c1; h2 ^= k2;
case 8: k1 ^= ((uint64_t)tail[ 7]) << 56;
case 7: k1 ^= ((uint64_t)tail[ 6]) << 48;
case 6: k1 ^= ((uint64_t)tail[ 5]) << 40;
case 5: k1 ^= ((uint64_t)tail[ 4]) << 32;
case 4: k1 ^= ((uint64_t)tail[ 3]) << 24;
case 3: k1 ^= ((uint64_t)tail[ 2]) << 16;
case 2: k1 ^= ((uint64_t)tail[ 1]) << 8;
case 1: k1 ^= ((uint64_t)tail[ 0]) << 0;
k1 *= c1; k1 = ROTL64(k1,31); k1 *= c2; h1 ^= k1;
};
//----------
// finalization
h1 ^= len; h2 ^= len;
h1 += h2;
h2 += h1;
h1 = fmix64(h1);
h2 = fmix64(h2);
h1 += h2;
h2 += h1;
((uint64_t*)out)[0] = h1;
((uint64_t*)out)[1] = h2;
}
//-----------------------------------------------------------------------------
src/mash/MurmurHash3.h deleted 100644 → 0
View file @ 076de3b2
//-----------------------------------------------------------------------------
// MurmurHash3 was written by Austin Appleby, and is placed in the public
// domain. The author hereby disclaims copyright to this source code.
#ifndef _MURMURHASH3_H_
#define _MURMURHASH3_H_
//-----------------------------------------------------------------------------
// Platform-specific functions and macros
// Microsoft Visual Studio
#if defined(_MSC_VER) && (_MSC_VER < 1600)
typedef unsigned char uint8_t;
typedef unsigned int uint32_t;
typedef unsigned __int64 uint64_t;
// Other compilers
#else // defined(_MSC_VER)
#include <stdint.h>
#endif // !defined(_MSC_VER)
//-----------------------------------------------------------------------------
void MurmurHash3_x86_32 ( const void * key, int len, uint32_t seed, void * out );
void MurmurHash3_x86_128 ( const void * key, int len, uint32_t seed, void * out );
void MurmurHash3_x64_128 ( const void * key, int len, uint32_t seed, void * out );
//-----------------------------------------------------------------------------
#endif // _MURMURHASH3_H_