New upstream version 1.4.1+git20181225.44d5a44+dfsg (ed2f52b0) · Commits · Debian Med / gatb-core

gatb-core/.gitignore

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		CMakeLists.txt.user
		/build*
		/.settings/
		/.cproject
		*.leon
		.DS_Store

gatb-core/cmake/CppUnit.cmake

+6 −3

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		@@ -3,6 +3,7 @@
		################################################################################

		FIND_PATH (CPPUNIT_INCLUDE_DIR cppunit/extensions/HelperMacros.h
		$ENV{HOME}/include
		$ENV{HOME}/.linuxbrew/include
		/local/include
		/usr/include
		@@ -18,10 +19,12 @@ FIND_LIBRARY (CPPUNIT_LIBRARY cppunit
		)

		# A little hack here... We check whether the static library is reachable too.
		IF (EXISTS "${CPPUNIT_INCLUDE_DIR}/cppunit/extensions/HelperMacros.h")
		if (NOT EXISTS "${CPPUNIT_INCLUDE_DIR}/../lib/libcppunit.a")
		message ("-- CppUnit: found headers (in ${CPPUNIT_INCLUDE_DIR}) but not the static library (${CPPUNIT_INCLUDE_DIR}/../lib/libcppunit.a)")
		SET (CPPUNIT_NO_STATIC_LIB_FOUND 1)
		endif()
		endif()

		IF (CPPUNIT_INCLUDE_DIR)
		IF (CPPUNIT_LIBRARY)

gatb-core/doc/book/.gitignore

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		/main.aux
		/main.log
		/main.pdf

gatb-core/examples/bank/bank18.cpp

+8 −4

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		@@ -42,12 +42,16 @@ int main (int argc, char* argv[])
		IBank* bank2 = Bank::open (options->getStr(STR_BANK2)); LOCAL (bank2);

		// We iterate the two banks. Note how we provide two iterators from the two banks.
		PairedIterator<Sequence> itPair (bank1->iterator(), bank2->iterator());
		PairedIterator<Sequence> * itPair = new PairedIterator<Sequence> (bank1->iterator(), bank2->iterator());
		LOCAL(itPair);

		for (itPair.first(); !itPair.isDone(); itPair.next())
		ProgressIterator< std::pair <Sequence, Sequence>> progress_iter (itPair, "coucou la paire", bank1->estimateNbItems());


		for (progress_iter.first(); !progress_iter.isDone(); progress_iter.next())
		{
		Sequence& s1 = itPair.item().first;
		Sequence& s2 = itPair.item().second;
		Sequence& s1 = itPair->item().first;
		Sequence& s2 = itPair->item().second;

		std::cout << "seq1.len=" << s1.getDataSize() << " seq2.len=" << s2.getDataSize() << std::endl;
		}

gatb-core/examples/protos/histo2D.cpp

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		/*
		* KAT-like analysis of a genome assembly
		*
		* given 2 datasets
		* outputs the 2D histogram of kmers
		*
		* must give 2 datasets, first readset, then genome
		* Sample command: histo2D -in readset.fasta,genome.fasta -kmer-size 25 > resultfile
		*
		*/
		#include <gatb/gatb_core.hpp>
		using namespace std;

		int dim1 = 10000; // max kmer occurence in read set
		int dim2 = 10; // max kmer occurence in genome

		#define IDX(i,j) ((i) + (j)*dim1)

		/********************************************************************************/
		template<size_t span>
		class CountProcessorCustom : public CountProcessorAbstract<span>
		{
		public:

		// We need the kmer size to dump kmers values as nucl strings
		CountProcessorCustom (size_t kmerSize, ISynchronizer* synchro, u_int64_t * histo_table_2D) : kmerSize(kmerSize), synchro(synchro), _histo_table_2D(histo_table_2D) {}

		virtual ~CountProcessorCustom () {}

		CountProcessorAbstract<span>* clone () { return new CountProcessorCustom<span>(kmerSize, synchro,_histo_table_2D); }

		virtual bool process (size_t partId, const typename Kmer<span>::Type& kmer, const CountVector& count, CountNumber sum)
		{
		if( count[0] < dim1 && count[1] < dim2)
		__sync_fetch_and_add ( & _histo_table_2D[IDX( count[0] , count[1] )], 1);
		return true;
		}

		private:
		size_t kmerSize;
		ISynchronizer *synchro;
		u_int64_t * _histo_table_2D;

		};

		/********************************************************************************/
		template<size_t span> struct MainLoop { void operator () (IProperties* options)
		{

		//check that the user gave 2 input banks
		std::string banknames = options->getStr(STR_URI_INPUT);
		size_t n = std::count(banknames.begin(), banknames.end(), ',');
		if( (n+1) != 2)
		{
		printf("There must be 2 input banks.\n");
		exit(1);
		}

		u_int64_t * histo_table_2D = (u_int64_t ) calloc( dim1 dim2 , sizeof(u_int64_t *));

		// We force the solidity kind (otherwise default value "sum" will consider N banks as a single one)
		options->setStr(STR_SOLIDITY_KIND, "all");

		// We create a SortingCountAlgorithm instance.
		SortingCountAlgorithm<span> algo (options);

		// global synchronization
		ISynchronizer* synchro = System::thread().newSynchronizer();

		// We create a custom count processor and give it to the sorting count algorithm
		algo.addProcessor (new CountProcessorCustom<span> (options->getInt(STR_KMER_SIZE), synchro,histo_table_2D));

		// We launch the algorithm
		algo.execute();

		//outptut the 2D histogram
		for(int ii=0; ii< dim1; ii++)
		{
		printf("%5i:\t",ii);
		for(int jj=0; jj< dim2; jj++)
		{
		printf("\t%6lli",histo_table_2D[IDX(ii,jj)]);
		}
		printf("\n");
		}
		free(histo_table_2D);

		}};

		/********************************************************************************/
		int main (int argc, char* argv[])
		{
		// We create a command line parser for the sorting count algorithm
		IOptionsParser* parser = SortingCountAlgorithm<>::getOptionsParser ();
		parser->push_back (new OptionOneParam (STR_NB_CORES, "nb cores", false, "1"));
		parser->push_back (new OptionOneParam (STR_VERBOSE, "verbosity", false, "1"));

		// We launch our functor
		return Algorithm::mainloop <MainLoop> (parser, argc, argv);
		}