Added support to transfer haplotypes once per region to the JNI
Re-use transferred haplotypes (stored in GlobalRef) across calls to computeLikelihoods
This commit is contained in:
Karthik Gururaj
parent
868a8394f7
commit
733a84e4f9
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@ -0,0 +1,76 @@
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#include "LoadTimeInitializer.h"
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#include "utils.h"
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using namespace std;
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LoadTimeInitializer g_load_time_initializer;
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LoadTimeInitializer::LoadTimeInitializer() //will be called when library is loaded
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{
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ConvertChar::init();
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m_sumNumReads = 0;
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m_sumSquareNumReads = 0;
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m_sumNumHaplotypes = 0;
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m_sumSquareNumHaplotypes = 0;
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m_sumNumTestcases = 0;
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m_sumSquareNumTestcases = 0;
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m_maxNumTestcases = 0;
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m_num_invocations = 0;
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m_compute_time = 0;
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m_data_transfer_time = 0;
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m_filename_to_fptr.clear();
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initialize_function_pointers();
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cout.flush();
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}
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void LoadTimeInitializer::print_profiling()
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{
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double mean_val;
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cout << "Compute time "<<m_compute_time<<"\n";
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cout << "Data initialization time "<<m_data_transfer_time<<"\n";
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cout <<"Invocations : "<<m_num_invocations<<"\n";
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cout << "term\tsum\tsumSq\tmean\tvar\tmax\n";
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mean_val = m_sumNumReads/m_num_invocations;
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cout << "reads\t"<<m_sumNumReads<<"\t"<<m_sumSquareNumReads<<"\t"<<mean_val<<"\t"<<
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(m_sumSquareNumReads/m_num_invocations)-mean_val*mean_val<<"\n";
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mean_val = m_sumNumHaplotypes/m_num_invocations;
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cout << "haplotypes\t"<<m_sumNumHaplotypes<<"\t"<<m_sumSquareNumHaplotypes<<"\t"<<mean_val<<"\t"<<
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(m_sumSquareNumHaplotypes/m_num_invocations)-mean_val*mean_val<<"\n";
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mean_val = m_sumNumTestcases/m_num_invocations;
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cout << "numtestcases\t"<<m_sumNumTestcases<<"\t"<<m_sumSquareNumTestcases<<"\t"<<mean_val<<"\t"<<
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(m_sumSquareNumTestcases/m_num_invocations)-mean_val*mean_val<<"\t"<<m_maxNumTestcases<<"\n";
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cout.flush();
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}
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void LoadTimeInitializer::debug_dump(string filename, string s, bool to_append, bool add_newline)
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{
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map<string, ofstream*>::iterator mI = m_filename_to_fptr.find(filename);
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ofstream* fptr = 0;
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if(mI == m_filename_to_fptr.end())
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{
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m_filename_to_fptr[filename] = new ofstream();
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fptr = m_filename_to_fptr[filename];
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fptr->open(filename.c_str(), to_append ? ios::app : ios::out);
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assert(fptr->is_open());
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}
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else
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fptr = (*mI).second;
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//ofstream fptr;
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//fptr.open(filename.c_str(), to_append ? ofstream::app : ofstream::out);
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(*fptr) << s;
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if(add_newline)
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(*fptr) << "\n";
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//fptr.close();
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}
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void LoadTimeInitializer::debug_close()
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{
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for(map<string,ofstream*>::iterator mB = m_filename_to_fptr.begin(), mE = m_filename_to_fptr.end();
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mB != mE;mB++)
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{
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(*mB).second->close();
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delete (*mB).second;
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}
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m_filename_to_fptr.clear();
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}
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@ -0,0 +1,37 @@
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#ifndef LOAD_TIME_INITIALIZER_H
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#define LOAD_TIME_INITIALIZER_H
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#include "headers.h"
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#include <jni.h>
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class LoadTimeInitializer
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{
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public:
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LoadTimeInitializer(); //will be called when library is loaded
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void print_profiling();
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void debug_dump(std::string filename, std::string s, bool to_append, bool add_newline=true);
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void debug_close();
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jfieldID m_readBasesFID;
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jfieldID m_readQualsFID;
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jfieldID m_insertionGOPFID;
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jfieldID m_deletionGOPFID;
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jfieldID m_overallGCPFID;
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jfieldID m_haplotypeBasesFID;
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//used to compute avg, variance of #testcases
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double m_sumNumReads;
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double m_sumSquareNumReads;
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double m_sumNumHaplotypes;
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double m_sumSquareNumHaplotypes;
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double m_sumNumTestcases;
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double m_sumSquareNumTestcases;
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unsigned m_maxNumTestcases;
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unsigned m_num_invocations;
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//timing
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double m_compute_time;
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double m_data_transfer_time;
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private:
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std::map<std::string, std::ofstream*> m_filename_to_fptr;
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};
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extern LoadTimeInitializer g_load_time_initializer;
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#endif
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@ -1,4 +1,5 @@
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#OMPCFLAGS=-fopenmp
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OMPCFLAGS=-fopenmp
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OMPLFLAGS=-fopenmp #-openmp-link static
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#CFLAGS=-O2 -std=c++11 -W -Wall -march=corei7-avx -Wa,-q -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
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#CFLAGS=-O2 -W -Wall -march=corei7 -mfpmath=sse -msse4.2 -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
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@ -19,7 +20,7 @@ DEPDIR=.deps
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DF=$(DEPDIR)/$(*).d
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#Common across libJNI and sandbox
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COMMON_SOURCES=utils.cc avx_function_instantiations.cc baseline.cc sse_function_instantiations.cc
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COMMON_SOURCES=utils.cc avx_function_instantiations.cc baseline.cc sse_function_instantiations.cc LoadTimeInitializer.cc
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#Part of libJNI
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LIBSOURCES=org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc $(COMMON_SOURCES)
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SOURCES=$(LIBSOURCES) pairhmm-template-main.cc pairhmm-1-base.cc
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@ -28,7 +29,7 @@ COMMON_OBJECTS=$(COMMON_SOURCES:.cc=.o)
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#No vectorization for these files
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NO_VECTOR_SOURCES=org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc pairhmm-template-main.cc pairhmm-1-base.cc utils.cc baseline.cc
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NO_VECTOR_SOURCES=org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc pairhmm-template-main.cc pairhmm-1-base.cc utils.cc baseline.cc LoadTimeInitializer.cc
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#Use -xAVX for these files
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AVX_SOURCES=avx_function_instantiations.cc
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#Use -xSSE4.2 for these files
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@ -47,13 +48,13 @@ all: $(BIN)
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-include $(addprefix $(DEPDIR)/,$(SOURCES:.cc=.d))
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checker: pairhmm-1-base.o $(COMMON_OBJECTS)
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$(CXX) $(OMPCFLAGS) -o $@ $^ $(LDFLAGS)
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$(CXX) $(OMPLFLAGS) -o $@ $^ $(LDFLAGS)
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pairhmm-template-main: pairhmm-template-main.o $(COMMON_OBJECTS)
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$(CXX) $(OMPCFLAGS) -o $@ $^ $(LDFLAGS)
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$(CXX) $(OMPLFLAGS) -o $@ $^ $(LDFLAGS)
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libJNILoglessPairHMM.so: $(LIBOBJECTS)
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$(CXX) $(OMPCFLAGS) -shared -o $@ $(LIBOBJECTS)
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$(CXX) $(OMPLFLAGS) -shared -o $@ $(LIBOBJECTS)
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$(OBJECTS): %.o: %.cc
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@ -11,96 +11,10 @@
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#include "template.h"
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#include "utils.h"
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#include "LoadTimeInitializer.h"
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using namespace std;
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class LoadTimeInitializer
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{
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public:
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LoadTimeInitializer() //will be called when library is loaded
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{
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ConvertChar::init();
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m_sumNumReads = 0;
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m_sumSquareNumReads = 0;
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m_sumNumHaplotypes = 0;
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m_sumSquareNumHaplotypes = 0;
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m_sumNumTestcases = 0;
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m_sumSquareNumTestcases = 0;
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m_maxNumTestcases = 0;
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m_num_invocations = 0;
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m_filename_to_fptr.clear();
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initialize_function_pointers();
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cout.flush();
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}
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void print_profiling()
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{
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double mean_val;
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cout <<"Invocations : "<<m_num_invocations<<"\n";
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cout << "term\tsum\tsumSq\tmean\tvar\tmax\n";
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mean_val = m_sumNumReads/m_num_invocations;
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cout << "reads\t"<<m_sumNumReads<<"\t"<<m_sumSquareNumReads<<"\t"<<mean_val<<"\t"<<
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(m_sumSquareNumReads/m_num_invocations)-mean_val*mean_val<<"\n";
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mean_val = m_sumNumHaplotypes/m_num_invocations;
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cout << "haplotypes\t"<<m_sumNumHaplotypes<<"\t"<<m_sumSquareNumHaplotypes<<"\t"<<mean_val<<"\t"<<
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(m_sumSquareNumHaplotypes/m_num_invocations)-mean_val*mean_val<<"\n";
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mean_val = m_sumNumTestcases/m_num_invocations;
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cout << "numtestcases\t"<<m_sumNumTestcases<<"\t"<<m_sumSquareNumTestcases<<"\t"<<mean_val<<"\t"<<
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(m_sumSquareNumTestcases/m_num_invocations)-mean_val*mean_val<<"\t"<<m_maxNumTestcases<<"\n";
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cout.flush();
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}
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void debug_dump(string filename, string s, bool to_append, bool add_newline=true)
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{
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map<string, ofstream*>::iterator mI = m_filename_to_fptr.find(filename);
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ofstream* fptr = 0;
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if(mI == m_filename_to_fptr.end())
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{
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m_filename_to_fptr[filename] = new ofstream();
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fptr = m_filename_to_fptr[filename];
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fptr->open(filename.c_str(), to_append ? ios::app : ios::out);
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assert(fptr->is_open());
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}
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else
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fptr = (*mI).second;
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//ofstream fptr;
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//fptr.open(filename.c_str(), to_append ? ofstream::app : ofstream::out);
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(*fptr) << s;
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if(add_newline)
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(*fptr) << "\n";
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//fptr.close();
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}
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void debug_close()
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{
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for(map<string,ofstream*>::iterator mB = m_filename_to_fptr.begin(), mE = m_filename_to_fptr.end();
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mB != mE;mB++)
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{
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(*mB).second->close();
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delete (*mB).second;
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}
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m_filename_to_fptr.clear();
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}
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jfieldID m_readBasesFID;
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jfieldID m_readQualsFID;
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jfieldID m_insertionGOPFID;
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jfieldID m_deletionGOPFID;
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jfieldID m_overallGCPFID;
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jfieldID m_haplotypeBasesFID;
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//used to compute avg, variance of #testcases
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double m_sumNumReads;
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double m_sumSquareNumReads;
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double m_sumNumHaplotypes;
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double m_sumSquareNumHaplotypes;
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double m_sumNumTestcases;
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double m_sumSquareNumTestcases;
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unsigned m_maxNumTestcases;
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unsigned m_num_invocations;
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private:
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map<string, ofstream*> m_filename_to_fptr;
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};
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LoadTimeInitializer g_load_time_initializer;
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializeProbabilities
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(JNIEnv* env, jclass thisObject,
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jobjectArray transition, jbyteArray insertionGOP, jbyteArray deletionGOP, jbyteArray overallGCP
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@ -128,7 +42,7 @@ Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializePrior
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//Gets direct access to Java arrays
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#define GET_BYTE_ARRAY_ELEMENTS env->GetPrimitiveArrayCritical
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#define RELEASE_BYTE_ARRAY_ELEMENTS env->ReleasePrimitiveArrayCritical
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#define JNI_RELEASE_MODE 0
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#define JNI_RO_RELEASE_MODE JNI_ABORT
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#define GET_DOUBLE_ARRAY_ELEMENTS env->GetPrimitiveArrayCritical
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#define RELEASE_DOUBLE_ARRAY_ELEMENTS env->ReleasePrimitiveArrayCritical
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@ -136,7 +50,7 @@ Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializePrior
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//Likely makes copy of Java arrays to JNI C++ space
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#define GET_BYTE_ARRAY_ELEMENTS env->GetByteArrayElements
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#define RELEASE_BYTE_ARRAY_ELEMENTS env->ReleaseByteArrayElements
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#define JNI_RELEASE_MODE JNI_ABORT
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#define JNI_RO_RELEASE_MODE JNI_ABORT
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#define GET_DOUBLE_ARRAY_ELEMENTS env->GetDoubleArrayElements
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#define RELEASE_DOUBLE_ARRAY_ELEMENTS env->ReleaseDoubleArrayElements
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@ -187,12 +101,12 @@ Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniSubComputeReadL
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#endif
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RELEASE_BYTE_ARRAY_ELEMENTS(overallGCP, overallGCPArray, JNI_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(deletionGOP, deletionGOPArray, JNI_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(insertionGOP, insertionGOPArray, JNI_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(readQuals, readQualsArray, JNI_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(haplotypeBases, haplotypeBasesArray, JNI_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(readBases, readBasesArray, JNI_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(overallGCP, overallGCPArray, JNI_RO_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(deletionGOP, deletionGOPArray, JNI_RO_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(insertionGOP, insertionGOPArray, JNI_RO_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(readQuals, readQualsArray, JNI_RO_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(haplotypeBases, haplotypeBasesArray, JNI_RO_RELEASE_MODE);
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RELEASE_BYTE_ARRAY_ELEMENTS(readBases, readBasesArray, JNI_RO_RELEASE_MODE);
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return 0.0;
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}
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@ -226,6 +140,46 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
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g_load_time_initializer.m_haplotypeBasesFID = fid;
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}
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//Since the list of haplotypes against which the reads are evaluated in PairHMM is the same for a region,
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//transfer the list only once
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vector<pair<jbyteArray, jbyte*> > g_haplotypeBasesArrayVector;
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializeHaplotypes
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(JNIEnv * env, jobject thisObject, jint numHaplotypes, jobjectArray haplotypeDataArray)
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{
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jboolean is_copy = JNI_FALSE;
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//To ensure, GET_BYTE_ARRAY_ELEMENTS is invoked only once for each haplotype, store bytearrays in a vector
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vector<pair<jbyteArray, jbyte*> >& haplotypeBasesArrayVector = g_haplotypeBasesArrayVector;
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haplotypeBasesArrayVector.clear();
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haplotypeBasesArrayVector.resize(numHaplotypes);
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for(unsigned j=0;j<numHaplotypes;++j)
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{
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jobject haplotypeObject = env->GetObjectArrayElement(haplotypeDataArray, j);
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jbyteArray haplotypeBases = (jbyteArray)env->GetObjectField(haplotypeObject, g_load_time_initializer.m_haplotypeBasesFID);
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#ifdef ENABLE_ASSERTIONS
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assert(haplotypeBases && ("haplotypeBases is NULL at index : "+to_string(j)+"\n").c_str());
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#endif
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//Need a global reference as this will be accessed across multiple JNI calls to JNIComputeLikelihoods()
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jbyteArray haplotypeBasesGlobalRef = (jbyteArray)env->NewGlobalRef(haplotypeBases);
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#ifdef ENABLE_ASSERTIONS
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assert(haplotypeBasesGlobalRef && ("Could not get global ref to haplotypeBases at index : "+to_string(j)+"\n").c_str());
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#endif
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env->DeleteLocalRef(haplotypeBases); //free the local reference
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jbyte* haplotypeBasesArray = (jbyte*)GET_BYTE_ARRAY_ELEMENTS(haplotypeBasesGlobalRef, &is_copy);
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#ifdef ENABLE_ASSERTIONS
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assert(haplotypeBasesArray && "haplotypeBasesArray not initialized in JNI");
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assert(env->GetArrayLength(haplotypeBasesGlobalRef) < MCOLS);
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#endif
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#ifdef DEBUG0_1
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cout << "JNI haplotype length "<<env->GetArrayLength(haplotypeBasesGlobalRef)<<"\n";
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#endif
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haplotypeBasesArrayVector[j] = make_pair(haplotypeBasesGlobalRef, haplotypeBasesArray);
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#ifdef DEBUG3
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for(unsigned k=0;k<env->GetArrayLength(haplotypeBases);++k)
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g_load_time_initializer.debug_dump("haplotype_bases_jni.txt",to_string((int)haplotypeBasesArray[k]),true);
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#endif
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}
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}
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//JNI function to invoke compute_full_prob_avx
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//readDataArray - array of JNIReadDataHolderClass objects which contain the readBases, readQuals etc
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//haplotypeDataArray - array of JNIHaplotypeDataHolderClass objects which contain the haplotypeBases
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@ -235,37 +189,16 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
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(JNIEnv* env, jobject thisObject, jint numReads, jint numHaplotypes,
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jobjectArray readDataArray, jobjectArray haplotypeDataArray, jdoubleArray likelihoodArray, jint maxNumThreadsToUse)
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{
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jboolean is_copy = JNI_FALSE;
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//To ensure, GET_BYTE_ARRAY_ELEMENTS is invoked only once for each haplotype, store bytearrays in a vector
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vector<pair<jbyteArray, jbyte*> > haplotypeBasesArrayVector;
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haplotypeBasesArrayVector.clear();
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haplotypeBasesArrayVector.resize(numHaplotypes);
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#ifdef DEBUG0_1
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cout << "JNI numReads "<<numReads<<" numHaplotypes "<<numHaplotypes<<"\n";
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#endif
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for(unsigned j=0;j<numHaplotypes;++j)
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{
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jobject haplotypeObject = env->GetObjectArrayElement(haplotypeDataArray, j);
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jbyteArray haplotypeBases = (jbyteArray)env->GetObjectField(haplotypeObject, g_load_time_initializer.m_haplotypeBasesFID);
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#ifdef ENABLE_ASSERTIONS
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assert(haplotypeBases && ("haplotypeBases is NULL at index : "+to_string(j)+"\n").c_str());
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#endif
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jbyte* haplotypeBasesArray = (jbyte*)GET_BYTE_ARRAY_ELEMENTS(haplotypeBases, &is_copy);
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#ifdef ENABLE_ASSERTIONS
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assert(haplotypeBasesArray && "haplotypeBasesArray not initialized in JNI");
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assert(env->GetArrayLength(haplotypeBases) < MCOLS);
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#endif
|
||||
#ifdef DEBUG0_1
|
||||
cout << "JNI haplotype length "<<env->GetArrayLength(haplotypeBases)<<"\n";
|
||||
#endif
|
||||
haplotypeBasesArrayVector[j] = make_pair(haplotypeBases, haplotypeBasesArray);
|
||||
#ifdef DEBUG3
|
||||
for(unsigned k=0;k<env->GetArrayLength(haplotypeBases);++k)
|
||||
g_load_time_initializer.debug_dump("haplotype_bases_jni.txt",to_string((int)haplotypeBasesArray[k]),true);
|
||||
#endif
|
||||
}
|
||||
double start_time = 0;
|
||||
//haplotype vector from earlier store - note the reference to vector, not copying
|
||||
vector<pair<jbyteArray, jbyte*> >& haplotypeBasesArrayVector = g_haplotypeBasesArrayVector;
|
||||
jboolean is_copy = JNI_FALSE;
|
||||
|
||||
unsigned numTestCases = numReads*numHaplotypes;
|
||||
//vector to store results
|
||||
vector<testcase> tc_array;
|
||||
tc_array.clear();
|
||||
tc_array.resize(numTestCases);
|
||||
|
|
@ -274,6 +207,9 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
|
|||
vector<vector<pair<jbyteArray,jbyte*> > > readBasesArrayVector;
|
||||
readBasesArrayVector.clear();
|
||||
readBasesArrayVector.resize(numReads);
|
||||
#ifdef DO_PROFILING
|
||||
start_time = getCurrClk();
|
||||
#endif
|
||||
for(unsigned i=0;i<numReads;++i)
|
||||
{
|
||||
//Get bytearray fields from read
|
||||
|
|
@ -340,25 +276,30 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
|
|||
tc_array[tc_idx].d[k] = (int)deletionGOPArray[k];
|
||||
tc_array[tc_idx].c[k] = (int)overallGCPArray[k];
|
||||
}
|
||||
|
||||
++tc_idx;
|
||||
}
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(overallGCP, overallGCPArray, JNI_RELEASE_MODE); //order of GET-RELEASE is important
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(deletionGOP, deletionGOPArray, JNI_RELEASE_MODE);
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(insertionGOP, insertionGOPArray, JNI_RELEASE_MODE);
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(readQuals, readQualsArray, JNI_RELEASE_MODE);
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(overallGCP, overallGCPArray, JNI_RO_RELEASE_MODE); //order of GET-RELEASE is important
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(deletionGOP, deletionGOPArray, JNI_RO_RELEASE_MODE);
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(insertionGOP, insertionGOPArray, JNI_RO_RELEASE_MODE);
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(readQuals, readQualsArray, JNI_RO_RELEASE_MODE);
|
||||
|
||||
//Release readBases at end because it is used by compute_full_prob
|
||||
readBasesArrayVector[i].clear();
|
||||
readBasesArrayVector[i].resize(1);
|
||||
readBasesArrayVector[i][0] = make_pair(readBases, readBasesArray);
|
||||
}
|
||||
#ifdef DO_PROFILING
|
||||
g_load_time_initializer.m_data_transfer_time += (getCurrClk()-start_time);
|
||||
#endif
|
||||
|
||||
jdouble* likelihoodDoubleArray = (jdouble*)GET_DOUBLE_ARRAY_ELEMENTS(likelihoodArray, &is_copy);
|
||||
#ifdef ENABLE_ASSERTIONS
|
||||
assert(likelihoodDoubleArray && "likelihoodArray is NULL");
|
||||
assert(env->GetArrayLength(likelihoodArray) == numTestCases);
|
||||
#endif
|
||||
#ifdef DO_PROFILING
|
||||
start_time = getCurrClk();
|
||||
#endif
|
||||
#pragma omp parallel for schedule (dynamic,10) private(tc_idx) num_threads(maxNumThreadsToUse)
|
||||
for(tc_idx=0;tc_idx<numTestCases;++tc_idx)
|
||||
{
|
||||
|
|
@ -373,27 +314,31 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
|
|||
|
||||
likelihoodDoubleArray[tc_idx] = result;
|
||||
}
|
||||
#ifdef DO_PROFILING
|
||||
g_load_time_initializer.m_compute_time += (getCurrClk()-start_time);
|
||||
#endif
|
||||
#ifdef DEBUG
|
||||
for(tc_idx=0;tc_idx<numTestCases;++tc_idx)
|
||||
{
|
||||
g_load_time_initializer.debug_dump("return_values_jni.txt",to_string(likelihoodDoubleArray[tc_idx]),true);
|
||||
}
|
||||
#endif
|
||||
RELEASE_DOUBLE_ARRAY_ELEMENTS(likelihoodArray, likelihoodDoubleArray, 0);
|
||||
|
||||
#ifdef DO_PROFILING
|
||||
start_time = getCurrClk();
|
||||
#endif
|
||||
RELEASE_DOUBLE_ARRAY_ELEMENTS(likelihoodArray, likelihoodDoubleArray, 0); //release mode 0, copy back results to Java memory
|
||||
|
||||
//Release read arrays first
|
||||
for(int i=readBasesArrayVector.size()-1;i>=0;--i)//note the order - reverse of GET
|
||||
{
|
||||
for(int j=readBasesArrayVector[i].size()-1;j>=0;--j)
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(readBasesArrayVector[i][j].first, readBasesArrayVector[i][j].second, JNI_RELEASE_MODE);
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(readBasesArrayVector[i][j].first, readBasesArrayVector[i][j].second, JNI_RO_RELEASE_MODE);
|
||||
readBasesArrayVector[i].clear();
|
||||
}
|
||||
readBasesArrayVector.clear();
|
||||
|
||||
//Now release haplotype arrays
|
||||
for(int j=numHaplotypes-1;j>=0;--j) //note the order - reverse of GET
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(haplotypeBasesArrayVector[j].first, haplotypeBasesArrayVector[j].second, JNI_RELEASE_MODE);
|
||||
haplotypeBasesArrayVector.clear();
|
||||
#ifdef DO_PROFILING
|
||||
g_load_time_initializer.m_data_transfer_time += (getCurrClk()-start_time);
|
||||
#endif
|
||||
tc_array.clear();
|
||||
#ifdef DO_PROFILING
|
||||
g_load_time_initializer.m_sumNumReads += numReads;
|
||||
|
|
@ -411,6 +356,21 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
|
|||
#endif
|
||||
}
|
||||
|
||||
//Release haplotypes at the end of a region
|
||||
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniFinalizeRegion
|
||||
(JNIEnv * env, jobject thisObject)
|
||||
{
|
||||
vector<pair<jbyteArray, jbyte*> >& haplotypeBasesArrayVector = g_haplotypeBasesArrayVector;
|
||||
//Now release haplotype arrays
|
||||
for(int j=haplotypeBasesArrayVector.size()-1;j>=0;--j) //note the order - reverse of GET
|
||||
{
|
||||
RELEASE_BYTE_ARRAY_ELEMENTS(haplotypeBasesArrayVector[j].first, haplotypeBasesArrayVector[j].second, JNI_RO_RELEASE_MODE);
|
||||
env->DeleteGlobalRef(haplotypeBasesArrayVector[j].first); //free the global reference
|
||||
}
|
||||
haplotypeBasesArrayVector.clear();
|
||||
}
|
||||
|
||||
|
||||
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniClose
|
||||
(JNIEnv* env, jobject thisObject)
|
||||
{
|
||||
|
|
|
|||
|
|
@ -21,6 +21,34 @@ extern "C" {
|
|||
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToDeletion 4L
|
||||
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_deletionToDeletion
|
||||
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_deletionToDeletion 5L
|
||||
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_debug
|
||||
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_debug 0L
|
||||
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_verify
|
||||
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_verify 0L
|
||||
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_debug0_1
|
||||
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_debug0_1 0L
|
||||
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_debug1
|
||||
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_debug1 0L
|
||||
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_debug2
|
||||
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_debug2 0L
|
||||
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_debug3
|
||||
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_debug3 0L
|
||||
/*
|
||||
* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
|
||||
* Method: jniGlobalInit
|
||||
* Signature: (Ljava/lang/Class;Ljava/lang/Class;)V
|
||||
*/
|
||||
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniGlobalInit
|
||||
(JNIEnv *, jobject, jclass, jclass);
|
||||
|
||||
/*
|
||||
* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
|
||||
* Method: jniClose
|
||||
* Signature: ()V
|
||||
*/
|
||||
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniClose
|
||||
(JNIEnv *, jobject);
|
||||
|
||||
/*
|
||||
* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
|
||||
* Method: jniInitialize
|
||||
|
|
@ -45,39 +73,38 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
|
|||
JNIEXPORT jdouble JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializePriorsAndUpdateCells
|
||||
(JNIEnv *, jobject, jboolean, jint, jint, jbyteArray, jbyteArray, jbyteArray, jint);
|
||||
|
||||
|
||||
/*
|
||||
* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
|
||||
* Method: jniSubComputeReadLikelihoodGivenHaplotypeLog10
|
||||
* Signature: (II[B[B[B[B[B[BI)D
|
||||
*/
|
||||
JNIEXPORT jdouble JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10
|
||||
(JNIEnv *, jobject, jint, jint, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jint);
|
||||
(JNIEnv *, jobject, jint, jint, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jint);
|
||||
|
||||
/*
|
||||
* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
|
||||
* Method: jniGlobalInit
|
||||
* Signature: (Ljava/lang/Class;Ljava/lang/Class;)V
|
||||
* Method: jniInitializeHaplotypes
|
||||
* Signature: (I[Lorg/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM/JNIHaplotypeDataHolderClass;)V
|
||||
*/
|
||||
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniGlobalInit
|
||||
(JNIEnv *, jobject, jclass, jclass);
|
||||
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializeHaplotypes
|
||||
(JNIEnv *, jobject, jint, jobjectArray);
|
||||
|
||||
/*
|
||||
* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
|
||||
* Method: jniFinalizeRegion
|
||||
* Signature: ()V
|
||||
*/
|
||||
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniFinalizeRegion
|
||||
(JNIEnv *, jobject);
|
||||
|
||||
/*
|
||||
* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
|
||||
* Method: jniComputeLikelihoods
|
||||
* Signature: ([Lorg/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM/JNIReadDataHolderClass;[Lorg/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM/JNIHaplotypeDataHolderClass;[D)V
|
||||
* Signature: (II[Lorg/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM/JNIReadDataHolderClass;[Lorg/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM/JNIHaplotypeDataHolderClass;[DI)V
|
||||
*/
|
||||
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniComputeLikelihoods
|
||||
(JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jdoubleArray, jint);
|
||||
|
||||
/*
|
||||
* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
|
||||
* Method: jniClose
|
||||
* Signature: ()V
|
||||
*/
|
||||
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniClose
|
||||
(JNIEnv *, jobject);
|
||||
|
||||
#ifdef __cplusplus
|
||||
}
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -4,26 +4,15 @@
|
|||
#include "headers.h"
|
||||
#include "template.h"
|
||||
#include "utils.h"
|
||||
#include "LoadTimeInitializer.h"
|
||||
|
||||
using namespace std;
|
||||
class LoadTimeInitializer
|
||||
{
|
||||
public:
|
||||
LoadTimeInitializer() //will be called when library is loaded
|
||||
{
|
||||
ConvertChar::init();
|
||||
}
|
||||
};
|
||||
LoadTimeInitializer g_load_time_initializer;
|
||||
|
||||
|
||||
#define BATCH_SIZE 10000
|
||||
#define RUN_HYBRID
|
||||
|
||||
double getCurrClk() {
|
||||
struct timeval tv ;
|
||||
gettimeofday(&tv, NULL);
|
||||
return (double)tv.tv_sec + (double)tv.tv_usec / 1000000.0;
|
||||
}
|
||||
|
||||
|
||||
int main(int argc, char** argv)
|
||||
{
|
||||
|
|
@ -39,9 +28,6 @@ int main(int argc, char** argv)
|
|||
if(argc >= 4)
|
||||
chunk_size = strtol(argv[3],0,10);
|
||||
|
||||
|
||||
initialize_function_pointers();
|
||||
|
||||
std::ifstream ifptr;
|
||||
FILE* fptr = 0;
|
||||
if(use_old_read_testcase)
|
||||
|
|
|
|||
|
|
@ -10,14 +10,9 @@
|
|||
#define BATCH_SIZE 10000
|
||||
#define RUN_HYBRID
|
||||
|
||||
double getCurrClk();
|
||||
int thread_level_parallelism_enabled = false ;
|
||||
|
||||
double getCurrClk() {
|
||||
struct timeval tv ;
|
||||
gettimeofday(&tv, NULL);
|
||||
return (double)tv.tv_sec + (double)tv.tv_usec / 1000000.0;
|
||||
}
|
||||
|
||||
void print128b_F(__m128 x)
|
||||
{
|
||||
float *p = (float *)(&x);
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
#!/bin/bash
|
||||
rm -f *.txt
|
||||
export GSA_ROOT_DIR=/home/karthikg/broad/gsa-unstable
|
||||
rm -f *.txt *.log
|
||||
GSA_ROOT_DIR=/home/karthikg/broad/gsa-unstable
|
||||
#-Djava.library.path is needed if you are using JNI_LOGLESS_CACHING, else not needed
|
||||
java -Djava.library.path=${GSA_ROOT_DIR}/PairHMM_JNI -jar $GSA_ROOT_DIR/dist/GenomeAnalysisTK.jar -T HaplotypeCaller \
|
||||
-R /opt/Genomics/ohsu/dnapipeline/humanrefgenome/human_g1k_v37.fasta \
|
||||
|
|
|
|||
|
|
@ -240,3 +240,8 @@ int read_mod_testcase(ifstream& fptr, testcase* tc, bool reformat)
|
|||
return tokens.size();
|
||||
}
|
||||
|
||||
double getCurrClk() {
|
||||
struct timeval tv ;
|
||||
gettimeofday(&tv, NULL);
|
||||
return (double)tv.tv_sec + (double)tv.tv_usec / 1000000.0;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
#ifndef PAIRHMM_UTIL_H
|
||||
#define PAIRHMM_UTIL_H
|
||||
|
||||
#include "template.h"
|
||||
|
||||
template<class T>
|
||||
std::string to_string(T obj)
|
||||
|
|
@ -25,4 +26,5 @@ void debug_dump(std::string filename, std::string s, bool to_append, bool add_ne
|
|||
template<class NUMBER>
|
||||
NUMBER compute_full_prob(testcase *tc, NUMBER *before_last_log=0);
|
||||
void initialize_function_pointers();
|
||||
double getCurrClk();
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -335,6 +335,11 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
|
|||
pairHMMThreadLocal.get().initialize(haplotypes, perSampleReadList, X_METRIC_LENGTH, Y_METRIC_LENGTH);
|
||||
}
|
||||
|
||||
private void finalizePairHMM()
|
||||
{
|
||||
pairHMMThreadLocal.get().finalizeRegion();
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public Map<String, PerReadAlleleLikelihoodMap> computeReadLikelihoods( final AssemblyResultSet assemblyResultSet, final Map<String, List<GATKSAMRecord>> perSampleReadList ) {
|
||||
|
|
@ -352,6 +357,9 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
|
|||
map.filterPoorlyModelledReads(EXPECTED_ERROR_RATE_PER_BASE);
|
||||
stratifiedReadMap.put(sampleEntry.getKey(), map);
|
||||
}
|
||||
|
||||
//Used mostly by the JNI implementation(s) to free arrays
|
||||
finalizePairHMM();
|
||||
|
||||
return stratifiedReadMap;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -68,8 +68,8 @@ import java.util.HashMap;
|
|||
public class JNILoglessPairHMM extends LoglessPairHMM {
|
||||
|
||||
private static final boolean debug = false; //simulates ifdef
|
||||
private static final boolean verify = debug || false; //simulates ifdef
|
||||
private static final boolean debug0_1 = false; //simulates ifdef
|
||||
private static final boolean verify = debug || true; //simulates ifdef
|
||||
private static final boolean debug0_1 = true; //simulates ifdef
|
||||
private static final boolean debug1 = false; //simulates ifdef
|
||||
private static final boolean debug2 = false;
|
||||
private static final boolean debug3 = false;
|
||||
|
|
@ -148,10 +148,10 @@ public class JNILoglessPairHMM extends LoglessPairHMM {
|
|||
jniInitialize(readMaxLength, haplotypeMaxLength);
|
||||
}
|
||||
|
||||
private native void jniInitialize(final int numHaplotypes, final int numTotalReads, JNIHaplotypeDataHolderClass[] haplotypeDataArray,
|
||||
JNIReadDataHolderClass[] readDataArray);
|
||||
HashMap<String, Integer> sampleToIndex = new HashMap<String, Integer>();
|
||||
//Used to transfer data to JNI
|
||||
private HashMap<Haplotype,Integer> haplotypeToHaplotypeListIdxMap = new HashMap<Haplotype,Integer>();
|
||||
private native void jniInitializeHaplotypes(final int numHaplotypes, JNIHaplotypeDataHolderClass[] haplotypeDataArray);
|
||||
//Used to transfer data to JNI
|
||||
//Since the haplotypes are the same for all calls to computeLikelihoods within a region, transfer the haplotypes only once to the JNI per region
|
||||
/**
|
||||
* {@inheritDoc}
|
||||
*/
|
||||
|
|
@ -159,7 +159,6 @@ public class JNILoglessPairHMM extends LoglessPairHMM {
|
|||
public void initialize( final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList, final int readMaxLength, final int haplotypeMaxLength ) {
|
||||
if(verify)
|
||||
super.initialize(haplotypes, perSampleReadList, readMaxLength, haplotypeMaxLength);
|
||||
/*
|
||||
int numHaplotypes = haplotypes.size();
|
||||
JNIHaplotypeDataHolderClass[] haplotypeDataArray = new JNIHaplotypeDataHolderClass[numHaplotypes];
|
||||
int idx = 0;
|
||||
|
|
@ -167,32 +166,22 @@ public class JNILoglessPairHMM extends LoglessPairHMM {
|
|||
{
|
||||
haplotypeDataArray[idx] = new JNIHaplotypeDataHolderClass();
|
||||
haplotypeDataArray[idx].haplotypeBases = currHaplotype.getBases();
|
||||
haplotypeToHaplotypeListIdxMap.put(currHaplotype, idx);
|
||||
++idx;
|
||||
}
|
||||
sampleToIndex.clear();
|
||||
int totalNumReads = 0;
|
||||
for(final Map.Entry<String, List<GATKSAMRecord>> currEntry : perSampleReadList)
|
||||
{
|
||||
sampleToIndex.put(currEntry.getKey(), totalNumReads);
|
||||
totalNumReads += currEntry.getValue().size();
|
||||
}
|
||||
jniInitializeHaplotypes(numHaplotypes, haplotypeDataArray);
|
||||
}
|
||||
|
||||
JNIHaplotypeDataHolderClass[] readDataArray = new JNIReadDataHolderClass[totalNumReads];
|
||||
idx = 0;
|
||||
for(final Map.Entry<String, List<GATKSAMRecord>> currEntry : perSampleReadList)
|
||||
{
|
||||
for(GATKSAMRecord read : currEntry.getValue())
|
||||
{
|
||||
readDataArray[idx] = new JNIReadDataHolderClass();
|
||||
readDataArray[idx].readBases = read.getReadBases();
|
||||
readDataArray[idx].readQuals = read.getBaseQualities();
|
||||
readDataArray[idx].insertionGOP = read.getBaseInsertionQualities();
|
||||
readDataArray[idx].deletionGOP = read.getBaseDeletionQualities();
|
||||
readDataArray[idx].overallGCP = GCPArrayMap.get(read);
|
||||
++idx;
|
||||
}
|
||||
}
|
||||
jniInitialize(numHaplotypes, numTotalReads, haplotypeDataArray, readDataArray);*/
|
||||
private native void jniFinalizeRegion();
|
||||
//Tell JNI to release arrays - really important if native code is directly accessing Java memory, if not
|
||||
//accessing Java memory directly, still important to release memory from C++
|
||||
/**
|
||||
* {@inheritDoc}
|
||||
*/
|
||||
@Override
|
||||
public void finalizeRegion()
|
||||
{
|
||||
jniFinalizeRegion();
|
||||
}
|
||||
|
||||
//Real compute kernel
|
||||
|
|
@ -216,10 +205,10 @@ public class JNILoglessPairHMM extends LoglessPairHMM {
|
|||
throw new IllegalStateException("Must call initialize before calling jniComputeLikelihoods in debug/verify mode");
|
||||
}
|
||||
int readListSize = reads.size();
|
||||
int alleleHaplotypeMapSize = alleleHaplotypeMap.size();
|
||||
int numTestcases = readListSize*alleleHaplotypeMapSize;
|
||||
int numHaplotypes = alleleHaplotypeMap.size();
|
||||
int numTestcases = readListSize*numHaplotypes;
|
||||
if(debug0_1)
|
||||
System.out.println("Java numReads "+readListSize+" numHaplotypes "+alleleHaplotypeMapSize);
|
||||
System.out.println("Java numReads "+readListSize+" numHaplotypes "+numHaplotypes);
|
||||
JNIReadDataHolderClass[] readDataArray = new JNIReadDataHolderClass[readListSize];
|
||||
int idx = 0;
|
||||
for(GATKSAMRecord read : reads)
|
||||
|
|
@ -246,39 +235,68 @@ public class JNILoglessPairHMM extends LoglessPairHMM {
|
|||
}
|
||||
++idx;
|
||||
}
|
||||
JNIHaplotypeDataHolderClass[] haplotypeDataArray = new JNIHaplotypeDataHolderClass[alleleHaplotypeMapSize];
|
||||
idx = 0;
|
||||
for (Map.Entry<Allele, Haplotype> currEntry : alleleHaplotypeMap.entrySet()) //order is important - access in same order always
|
||||
|
||||
JNIHaplotypeDataHolderClass[] haplotypeDataArray = new JNIHaplotypeDataHolderClass[numHaplotypes];
|
||||
if(verify)
|
||||
{
|
||||
haplotypeDataArray[idx] = new JNIHaplotypeDataHolderClass();
|
||||
haplotypeDataArray[idx].haplotypeBases = currEntry.getValue().getBases();
|
||||
if(debug0_1)
|
||||
System.out.println("Java haplotype length "+haplotypeDataArray[idx].haplotypeBases.length);
|
||||
if(debug3)
|
||||
idx = 0;
|
||||
for (Map.Entry<Allele, Haplotype> currEntry : alleleHaplotypeMap.entrySet()) //order is important - access in same order always
|
||||
{
|
||||
for(int i=0;i<haplotypeDataArray[idx].haplotypeBases.length;++i)
|
||||
debugDump("haplotype_bases_java.txt",String.format("%d\n",(int)haplotypeDataArray[idx].haplotypeBases[i]),true);
|
||||
haplotypeDataArray[idx] = new JNIHaplotypeDataHolderClass();
|
||||
haplotypeDataArray[idx].haplotypeBases = currEntry.getValue().getBases();
|
||||
if(debug0_1)
|
||||
System.out.println("Java haplotype length "+haplotypeDataArray[idx].haplotypeBases.length);
|
||||
if(debug3)
|
||||
{
|
||||
for(int i=0;i<haplotypeDataArray[idx].haplotypeBases.length;++i)
|
||||
debugDump("haplotype_bases_java.txt",String.format("%d\n",(int)haplotypeDataArray[idx].haplotypeBases[i]),true);
|
||||
}
|
||||
++idx;
|
||||
}
|
||||
++idx;
|
||||
}
|
||||
double[] likelihoodArray = new double[readListSize*alleleHaplotypeMapSize]; //to store results
|
||||
double[] likelihoodArray = new double[readListSize*numHaplotypes]; //to store results
|
||||
//for(reads)
|
||||
// for(haplotypes)
|
||||
// compute_full_prob()
|
||||
jniComputeLikelihoods(readListSize, alleleHaplotypeMapSize, readDataArray, haplotypeDataArray, likelihoodArray, 12);
|
||||
jniComputeLikelihoods(readListSize, numHaplotypes, readDataArray, haplotypeDataArray, likelihoodArray, 12);
|
||||
|
||||
|
||||
//final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap();
|
||||
PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap();
|
||||
idx = 0;
|
||||
int idxInsideHaplotypeList = 0;
|
||||
int readIdx = 0;
|
||||
for(GATKSAMRecord read : reads)
|
||||
{
|
||||
for (Map.Entry<Allele, Haplotype> currEntry : alleleHaplotypeMap.entrySet())//order is important - access in same order always
|
||||
{
|
||||
likelihoodMap.add(read, currEntry.getKey(), likelihoodArray[idx]);
|
||||
//Since the order of haplotypes in the List<Haplotype> and alleleHaplotypeMap is different,
|
||||
//get idx of current haplotype in the list and use this idx to get the right likelihoodValue
|
||||
idxInsideHaplotypeList = haplotypeToHaplotypeListIdxMap.get(currEntry.getValue());
|
||||
likelihoodMap.add(read, currEntry.getKey(), likelihoodArray[readIdx + idxInsideHaplotypeList]);
|
||||
++idx;
|
||||
}
|
||||
readIdx += numHaplotypes;
|
||||
}
|
||||
if(verify)
|
||||
{
|
||||
//re-order values in likelihoodArray
|
||||
double[] tmpArray = new double[numHaplotypes];
|
||||
idx = 0;
|
||||
idxInsideHaplotypeList = 0;
|
||||
readIdx = 0;
|
||||
for(GATKSAMRecord read : reads)
|
||||
{
|
||||
for(int j=0;j<numHaplotypes;++j)
|
||||
tmpArray[j] = likelihoodArray[readIdx+j];
|
||||
for (Map.Entry<Allele, Haplotype> currEntry : alleleHaplotypeMap.entrySet())//order is important - access in same order always
|
||||
{
|
||||
idxInsideHaplotypeList = haplotypeToHaplotypeListIdxMap.get(currEntry.getValue());
|
||||
likelihoodArray[idx] = tmpArray[idxInsideHaplotypeList];
|
||||
++idx;
|
||||
}
|
||||
readIdx += numHaplotypes;
|
||||
}
|
||||
//to compare values
|
||||
likelihoodMap = super.computeLikelihoods(reads, alleleHaplotypeMap, GCPArrayMap);
|
||||
//for floating point values, no exact equality
|
||||
|
|
@ -304,23 +322,23 @@ public class JNILoglessPairHMM extends LoglessPairHMM {
|
|||
if(toDump)
|
||||
{
|
||||
idx = 0;
|
||||
System.out.println("Dump : Java numReads "+readListSize+" numHaplotypes "+alleleHaplotypeMapSize);
|
||||
System.out.println("Dump : Java numReads "+readListSize+" numHaplotypes "+numHaplotypes);
|
||||
for(int i=0;i<readDataArray.length;++i)
|
||||
{
|
||||
for(int j=0;j<haplotypeDataArray.length;++j)
|
||||
{
|
||||
debugDump("debug_dump.log",new String(haplotypeDataArray[j].haplotypeBases)+" ",true);
|
||||
debugDump("debug_dump.log",new String(readDataArray[i].readBases)+" ",true);
|
||||
debugDump("debug_dump.txt",new String(haplotypeDataArray[j].haplotypeBases)+" ",true);
|
||||
debugDump("debug_dump.txt",new String(readDataArray[i].readBases)+" ",true);
|
||||
for(int k=0;k<readDataArray[i].readBases.length;++k)
|
||||
debugDump("debug_dump.log",String.format("%d",(int)(readDataArray[i].readQuals[k]))+" ",true);
|
||||
debugDump("debug_dump.txt",String.format("%d",(int)(readDataArray[i].readQuals[k]))+" ",true);
|
||||
for(int k=0;k<readDataArray[i].readBases.length;++k)
|
||||
debugDump("debug_dump.log",String.format("%d",(int)(readDataArray[i].insertionGOP[k]))+" ",true);
|
||||
debugDump("debug_dump.txt",String.format("%d",(int)(readDataArray[i].insertionGOP[k]))+" ",true);
|
||||
for(int k=0;k<readDataArray[i].readBases.length;++k)
|
||||
debugDump("debug_dump.log",String.format("%d",(int)(readDataArray[i].deletionGOP[k]))+" ",true);
|
||||
debugDump("debug_dump.txt",String.format("%d",(int)(readDataArray[i].deletionGOP[k]))+" ",true);
|
||||
for(int k=0;k<readDataArray[i].readBases.length;++k)
|
||||
debugDump("debug_dump.log",String.format("%d",(int)(readDataArray[i].overallGCP[k]))+" ",true);
|
||||
debugDump("debug_dump.log","\n",true);
|
||||
debugDump("debug_results.log",String.format("%e %e\n",mLikelihoodArray[idx],likelihoodArray[idx]),true);
|
||||
debugDump("debug_dump.txt",String.format("%d",(int)(readDataArray[i].overallGCP[k]))+" ",true);
|
||||
debugDump("debug_dump.txt","\n",true);
|
||||
debugDump("debug_results.txt",String.format("%e %e\n",mLikelihoodArray[idx],likelihoodArray[idx]),true);
|
||||
++idx;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -100,6 +100,14 @@ public abstract class PairHMM {
|
|||
initialized = true;
|
||||
}
|
||||
|
||||
/**
|
||||
* Called at the end of PairHMM for a region - mostly used by the JNI implementations
|
||||
*/
|
||||
public void finalizeRegion()
|
||||
{
|
||||
;
|
||||
}
|
||||
|
||||
/**
|
||||
* Initialize this PairHMM, making it suitable to run against a read and haplotype with given lengths
|
||||
* This function is used by the JNI implementations to transfer all data once to the native code
|
||||
|
|
|
|||
Loading…
Reference in New Issue