87 lines
2.9 KiB
C++
87 lines
2.9 KiB
C++
/*Copyright (c) 2012 The Broad Institute
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*Permission is hereby granted, free of charge, to any person
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*obtaining a copy of this software and associated documentation
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*files (the "Software"), to deal in the Software without
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*restriction, including without limitation the rights to use,
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*copy, modify, merge, publish, distribute, sublicense, and/or sell
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*copies of the Software, and to permit persons to whom the
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*Software is furnished to do so, subject to the following
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*conditions:
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*The above copyright notice and this permission notice shall be
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*included in all copies or substantial portions of the Software.
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*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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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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/*#include "template.h"*/
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enum LoadTimeInitializerStatsEnum
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{
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NUM_REGIONS_IDX=0,
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NUM_READS_IDX,
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NUM_HAPLOTYPES_IDX,
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NUM_TESTCASES_IDX,
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NUM_DOUBLE_INVOCATIONS_IDX,
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HAPLOTYPE_LENGTH_IDX,
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READ_LENGTH_IDX,
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PRODUCT_READ_LENGTH_HAPLOTYPE_LENGTH_IDX,
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TOTAL_NUMBER_STATS
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};
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extern char* LoadTimeInitializerStatsNames[];
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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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void dump_sandbox(testcase& tc, unsigned tc_idx, unsigned numReads, unsigned numHaplotypes);
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void open_sandbox() { m_sandbox_fptr.open("sandbox.txt", std::ios::app); }
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void close_sandbox() { m_sandbox_fptr.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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//profiling - update stats
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void update_stat(LoadTimeInitializerStatsEnum stat_idx, uint64_t value);
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//timing in nanoseconds
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uint64_t m_compute_time;
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uint64_t m_data_transfer_time;
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//bytes copied
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uint64_t m_bytes_copied;
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private:
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std::map<std::string, std::ofstream*> m_filename_to_fptr;
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std::set<std::string> m_written_files_set;
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std::ofstream m_sandbox_fptr;
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//used to compute various stats
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uint64_t m_sum_stats[TOTAL_NUMBER_STATS];
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double m_sum_square_stats[TOTAL_NUMBER_STATS];
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uint64_t m_min_stats[TOTAL_NUMBER_STATS];
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uint64_t m_max_stats[TOTAL_NUMBER_STATS];
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};
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extern LoadTimeInitializer g_load_time_initializer;
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#define SIZE_PER_TESTCASE 6*10000
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#define SIZE_PER_BUFFER 10000
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#endif
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