[med-svn] [Git][med-team/gatb-core][upstream] New upstream version 1.4.2+dfsg
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Apr 13 12:04:28 BST 2020
Michael R. Crusoe pushed to branch upstream at Debian Med / gatb-core
Commits:
3fcc375e by Michael R. Crusoe at 2020-04-13T12:39:58+02:00
New upstream version 1.4.2+dfsg
- - - - -
19 changed files:
- + .circleci/config.yml
- − .travis.yml
- README.md
- gatb-core/CMakeLists.txt
- gatb-core/src/gatb/bank/impl/BankComposite.hpp
- gatb-core/src/gatb/bank/impl/BankFasta.hpp
- gatb-core/src/gatb/bank/impl/BankRandom.hpp
- gatb-core/src/gatb/bank/impl/BankSplitter.hpp
- gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp
- gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp
- gatb-core/src/gatb/tools/compression/HeaderCoder.cpp
- gatb-core/src/gatb/tools/compression/Leon.hpp
- gatb-core/src/gatb/tools/math/Integer.hpp
- gatb-core/src/gatb/tools/math/LargeInt.hpp
- gatb-core/src/gatb/tools/math/LargeInt1.pri
- gatb-core/src/gatb/tools/math/NativeInt64.hpp
- gatb-core/src/gatb/tools/math/NativeInt8.hpp
- gatb-core/src/gatb/tools/misc/impl/Pool.hpp
- gatb-core/thirdparty/BooPHF/BooPHF.h
Changes:
=====================================
.circleci/config.yml
=====================================
@@ -0,0 +1,37 @@
+version: 1
+jobs:
+ build:
+ docker:
+ - image: "debian:stretch"
+ steps:
+ - checkout
+ - run:
+ name: Installing SUDO
+ command: 'apt-get update && apt-get install -y sudo && rm -rf /var/lib/apt/lists/*'
+ - run:
+ name: Installing GCC
+ command: 'apt-get update && apt-get install -y build-essential wget zlib1g zlib1g-dev'
+ - run:
+ name: Install CMAKE
+ command: |
+ wget https://cmake.org/files/v3.10/cmake-3.10.2-Linux-x86_64.tar.gz
+ tar -xvzf cmake-3.10.2-Linux-x86_64.tar.gz
+ chmod +x ./cmake-3.10.2-Linux-x86_64/bin/ccmake
+ chmod +x ./cmake-3.10.2-Linux-x86_64/bin/cmake
+ chmod +x ./cmake-3.10.2-Linux-x86_64/bin/cpack
+ chmod +x ./cmake-3.10.2-Linux-x86_64/bin/ctest
+ DIR=$(pwd)
+ ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/ccmake /usr/bin/ccmake
+ ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/cmake /usr/bin/cmake
+ ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/cpack /usr/bin/cpack
+ ln -s $DIR/cmake-3.10.2-Linux-x86_64/bin/ctest /usr/bin/ctest
+ - run:
+ name: Install CPPUnit
+ command: 'apt-get update && sudo apt-get install -y libcppunit-dev'
+ - run:
+ name: Creating Build Files
+ command: 'cd gatb-core && mkdir build && cd build && cmake .. && make -j 4'
+ # looks like circleci charges credits so i better not run the cppunit tests..
+ # - run:
+ # name: CPPUnit test
+ # command: 'export CPPUNIT_VERBOSE=TRUE && cd gatb-core/build && ./bin/gatb-core-cppunit'
=====================================
.travis.yml deleted
=====================================
@@ -1,31 +0,0 @@
-language: cpp
-os:
-- linux
-compiler:
-- clang
-- gcc
-addons:
- apt:
- sources:
- - ubuntu-toolchain-r-test
- - llvm-toolchain-precise-3.7
- - george-edison55-precise-backports # for cmake 3
- packages:
- - libcppunit-dev
- - g++-4.8
- - clang-3.7
- - cmake
- - cmake-data
-install:
-- if [ "`echo $CXX`" == "g++" ] && [ "$TRAVIS_OS_NAME" == "linux" ]; then export CXX=g++-4.8; fi
-- if [ "`echo $CXX`" == "clang++" ] && [ "$TRAVIS_OS_NAME" == "linux" ]; then export CXX=clang++-3.7; fi
-matrix:
-script:
-- cd gatb-core
-- mkdir build
-- cd build
-- cmake .. && make
-- export CPPUNIT_VERBOSE=TRUE && ./bin/gatb-core-cppunit
-env:
- global:
- - MAKEFLAGS="-j 4"
=====================================
README.md
=====================================
@@ -77,7 +77,7 @@ generate the wanted artifacts:
The following third parties have to be already installed to compile GATB-Core:
* a **C++/11 capable compiler** (*e.g.* gcc 4.7+, clang 3.5+, Apple/clang 6.0+)
-* **CMake 3.1+**
+* **CMake 3.10+**
In addition, you could install these optional tools:
=====================================
gatb-core/CMakeLists.txt
=====================================
@@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 3.10.0)
# The default version number is the latest official build
SET (gatb-core_VERSION_MAJOR 1)
SET (gatb-core_VERSION_MINOR 4)
-SET (gatb-core_VERSION_PATCH 1)
+SET (gatb-core_VERSION_PATCH 2)
# But, it is possible to define another release number during a local build
IF (DEFINED MAJOR)
=====================================
gatb-core/src/gatb/bank/impl/BankComposite.hpp
=====================================
@@ -153,7 +153,7 @@ public:
size_t getCompositionNb() { return _banks.size(); }
/** \return maximum number of files. */
- static const size_t getMaxNbFiles () { return 30; }
+ static size_t getMaxNbFiles () { return 30; }
/** Return the vector of IBank objects.
* \return the IBank objects. */
=====================================
gatb-core/src/gatb/bank/impl/BankFasta.hpp
=====================================
@@ -209,7 +209,7 @@ public:
protected:
/** \return maximum number of files. */
- static const size_t getMaxNbFiles () { return 1; }
+ static size_t getMaxNbFiles () { return 1; }
friend class Iterator;
=====================================
gatb-core/src/gatb/bank/impl/BankRandom.hpp
=====================================
@@ -81,7 +81,7 @@ public:
void estimate (u_int64_t& number, u_int64_t& totalSize, u_int64_t& maxSize);
/** \return maximum number of files. */
- static const size_t getMaxNbFiles () { return 0; }
+ static size_t getMaxNbFiles () { return 0; }
/************************************************************/
=====================================
gatb-core/src/gatb/bank/impl/BankSplitter.hpp
=====================================
@@ -99,7 +99,7 @@ public:
void estimate (u_int64_t& number, u_int64_t& totalSize, u_int64_t& maxSize);
/** \return maximum number of files. */
- static const size_t getMaxNbFiles () { return 0; }
+ static size_t getMaxNbFiles () { return 0; }
/************************************************************/
=====================================
gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp
=====================================
@@ -119,7 +119,7 @@ public:
fprintf(histo2Dfile,"%5i:\t",ii);
for(int jj=0; jj<= _histogram->getLength2(); jj++)
{
- fprintf(histo2Dfile,"\t%6lli", _histogram->get2D(ii,jj));
+ fprintf(histo2Dfile,"\t%6lli", (long long)_histogram->get2D(ii,jj));
}
fprintf(histo2Dfile,"\n");
}
@@ -134,7 +134,7 @@ public:
//output 1D histogram now
for(int ii=1; ii<= _histogram->getLength(); ii++)
{
- fprintf(histo1Dfile,"%i\t%lli",ii,_histogram->get(ii));
+ fprintf(histo1Dfile,"%i\t%lli",ii,(long long)_histogram->get(ii));
fprintf(histo1Dfile,"\n");
}
=====================================
gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp
=====================================
@@ -81,7 +81,7 @@ namespace gatb { namespace core { namespace kmer { namespace impl {
static const char* progressFormat0 = "DSK: counting kmers ";
static const char* progressFormat1 = "DSK: Pass %d/%d, Step 1: partitioning ";
static const char* progressFormat2 = "DSK: Pass %d/%d, Step 2: counting kmers ";
-static const char* progressFormat4 = "DSK: nb solid kmers found : %-9ld ";
+static const char* progressFormat4 = "DSK: nb solid kmers: %-9ld ";
/*********************************************************************
** METHOD :
=====================================
gatb-core/src/gatb/tools/compression/HeaderCoder.cpp
=====================================
@@ -25,6 +25,7 @@
#define PRINT_DEBUG_ENCODER
#define PRINT_DEBUG_DECODER
*/
+#include <string>
//====================================================================================
@@ -703,13 +704,10 @@ void HeaderDecoder::decodeNumeric(){
u_int64_t value = CompressionUtils::decodeNumeric(_rangeDecoder, _numericModels[_misIndex]);
//_currentHeader += CompressionUtils::numberToString(value);
- char temp[200];
- snprintf(temp,200,"%llu",value);
- _currentHeader += string(temp);
- //_currentHeader += to_string(value); // C++11
+ _currentHeader += std::to_string(value);
#ifdef PRINT_DEBUG_DECODER
- cout << "\t\t\tAdding: " << string(temp) << endl;
+ cout << "\t\t\tAdding: " << std::to_string(value) << endl;
#endif
}
@@ -723,13 +721,10 @@ void HeaderDecoder::decodeDelta(){
value = CompressionUtils::getValueFromDelta(1, _prevFieldValues[_fieldIndex], value);
- char temp[200];
- snprintf(temp,200,"%llu",value);
- _currentHeader += string(temp);
- //_currentHeader += to_string(value);
+ _currentHeader += std::to_string(value);
#ifdef PRINT_DEBUG_DECODER
- cout << "\t\t\tAdding: " << string(temp) << endl;
+ cout << "\t\t\tAdding: " << std::to_string(value) << endl;
#endif
}
@@ -742,13 +737,10 @@ void HeaderDecoder::decodeDelta2(){
u_int64_t value = CompressionUtils::decodeNumeric(_rangeDecoder, _numericModels[_misIndex]);
value = CompressionUtils::getValueFromDelta(2, _prevFieldValues[_fieldIndex], value);
- char temp[200];
- snprintf(temp,200,"%llu",value);
- _currentHeader += string(temp);
- //_currentHeader += to_string(value);
+ _currentHeader += std::to_string(value);
#ifdef PRINT_DEBUG_DECODER
- cout << "\t\t\tAdding: " << string(temp) << endl;
+ cout << "\t\t\tAdding: " << std::to_string(value) << endl;
#endif
}
=====================================
gatb-core/src/gatb/tools/compression/Leon.hpp
=====================================
@@ -462,7 +462,7 @@ public:
void estimate (u_int64_t& number, u_int64_t& totalSize, u_int64_t& maxSize);
/** \return maximum number of files. */
- static const size_t getMaxNbFiles () { return 0; }
+ static size_t getMaxNbFiles () { return 0; }
/************************************************************/
=====================================
gatb-core/src/gatb/tools/math/Integer.hpp
=====================================
@@ -114,7 +114,7 @@ public:
/** Get the size of an instance of the class used by the variant (ie. one of the Ti template class parameters)
* \return the size of an object (in bits).
*/
- const size_t getSize () { return boost::apply_visitor (Integer_size(), *(*this)); }
+ size_t getSize () { return boost::apply_visitor (Integer_size(), *(*this)); }
/** Get the HDF5 type for the the class used by the variant (ie. one of the Ti template class parameters)
* \param[in] isCompound : tells whether the type is composed or not
@@ -310,7 +310,7 @@ private:
template<typename T> const char* operator() (const T& a) const { return a.getName(); }};
struct Integer_size : public boost::static_visitor<const size_t> {
- template<typename T> const size_t operator() (const T& a) const { return a.getSize(); }};
+ template<typename T> size_t operator() (const T& a) const { return a.getSize(); }};
struct Integer_plus : public boost::static_visitor<IntegerTemplate> {
template<typename T> IntegerTemplate operator() (const T& a, const T& b) const { return IntegerTemplate(a + b); }
=====================================
gatb-core/src/gatb/tools/math/LargeInt.hpp
=====================================
@@ -137,7 +137,7 @@ public:
/** Get the size of an instance of the class
* \return the size of an object (in bits).
*/
- static const size_t getSize () { return 8*sizeof(u_int64_t)*precision; }
+ static size_t getSize () { return 8*sizeof(u_int64_t)*precision; }
/********************************************************************************/
/** Returns lower 64 bits */
=====================================
gatb-core/src/gatb/tools/math/LargeInt1.pri
=====================================
@@ -46,7 +46,7 @@ public:
static const char* getName () { return "LargeInt<1>"; }
- static const size_t getSize () { return 8*sizeof(u_int64_t); }
+ static size_t getSize () { return 8*sizeof(u_int64_t); }
/** Returns lower 64 bits */
u_int64_t toInt () const { return value; }
=====================================
gatb-core/src/gatb/tools/math/NativeInt64.hpp
=====================================
@@ -59,7 +59,7 @@ public:
void setVal (u_int64_t c) { value = c; }
- static const size_t getSize () { return 8*sizeof(u_int64_t); }
+ static size_t getSize () { return 8*sizeof(u_int64_t); }
NativeInt64 operator+ (const NativeInt64& other) const { return value + other.value; }
NativeInt64 operator- (const NativeInt64& other) const { return value - other.value; }
=====================================
gatb-core/src/gatb/tools/math/NativeInt8.hpp
=====================================
@@ -51,7 +51,7 @@ public:
static const char* getName () { return "NativeInt8"; }
- static const size_t getSize () { return 8*sizeof(u_int8_t); }
+ static size_t getSize () { return 8*sizeof(u_int8_t); }
operator char () const { return (char) value[0]; }
=====================================
gatb-core/src/gatb/tools/misc/impl/Pool.hpp
=====================================
@@ -359,6 +359,12 @@ public:
capacity = size+extraMem;
mainbuffer = (char*) CALLOC(capacity,1);
used_space = 0;
+
+ if (mainbuffer == NULL)
+ {
+ throw system::Exception ("Pool reserve() failed for %lld (+ %lld extra for %d cores) bytes",
+ size, extraMem, _nbCores);
+ }
}
//should be thread safe
=====================================
gatb-core/thirdparty/BooPHF/BooPHF.h
=====================================
@@ -4,6 +4,7 @@
#pragma once
#include <stdio.h>
+#include <cinttypes>
#include <climits>
#include <stdlib.h>
#include <iostream>
@@ -532,11 +533,11 @@ we need this 2-functors scheme because HashFunctors won't work with unordered_ma
//for debug purposes
void print() const
{
- printf("bit array of size %lli: \n",_size);
+ printf("bit array of size %lld: \n",(long long)_size);
for(uint64_t ii = 0; ii< _size; ii++)
{
if(ii%10==0)
- printf(" (%llu) ",ii);
+ printf(" (%lld) ",(long long)ii);
int val = (_bitArray[ii >> 6] >> (ii & 63 ) ) & 1;
printf("%i",val);
}
@@ -545,7 +546,7 @@ we need this 2-functors scheme because HashFunctors won't work with unordered_ma
printf("rank array : size %lu \n",_ranks.size());
for (uint64_t ii = 0; ii< _ranks.size(); ii++)
{
- printf("%llu : %lli, ",ii,_ranks[ii]);
+ printf("%lld : %lld, ",(long long)ii,(long long)_ranks[ii]);
}
printf("\n");
}
@@ -836,7 +837,7 @@ we need this 2-functors scheme because HashFunctors won't work with unordered_ma
uint64_t totalsize = totalsizeBitset + _final_hash.size()*42*8 ; // unordered map takes approx 42B per elem [personal test] (42B with uint64_t key, would be larger for other type of elem)
- printf("Bitarray %12llu bits (%.2f %%) (array + ranks )\n",
+ printf("Bitarray %12" PRIu64 " bits (%.2f %%) (array + ranks )\n",
totalsizeBitset, 100*(float)totalsizeBitset/totalsize);
printf("final hash %12lu bits (%.2f %%) (nb in final hash %lu)\n",
_final_hash.size()*42*8, 100*(float)(_final_hash.size()*42*8)/totalsize,
View it on GitLab: https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f
--
View it on GitLab: https://salsa.debian.org/med-team/gatb-core/-/commit/3fcc375e5c77b3703a0742bf74b1e8f3ccd8fe3f
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