├── SATnano ├── build │ ├── CMakeFiles │ │ ├── Progress │ │ │ ├── 1 │ │ │ ├── 2 │ │ │ ├── 3 │ │ │ ├── 4 │ │ │ ├── 5 │ │ │ ├── 6 │ │ │ ├── 7 │ │ │ ├── 8 │ │ │ ├── 9 │ │ │ ├── 12 │ │ │ ├── 13 │ │ │ ├── 14 │ │ │ ├── 16 │ │ │ ├── 17 │ │ │ ├── 18 │ │ │ ├── 19 │ │ │ └── count.txt │ │ ├── progress.make │ │ ├── cmake.check_cache │ │ ├── CompilerIdC │ │ │ └── a.out │ │ ├── CompilerIdCXX │ │ │ └── a.out │ │ ├── CMakeDetermineCompilerABI_C.bin │ │ ├── CMakeDetermineCompilerABI_CXX.bin │ │ ├── CMakeSystem.cmake │ │ ├── CMakeCCompiler.cmake │ │ ├── CMakeDirectoryInformation.cmake │ │ ├── CMakeCXXCompiler.cmake │ │ ├── CMakeError.log │ │ └── Makefile.cmake │ ├── lib │ │ ├── CMakeFiles │ │ │ ├── progress.make │ │ │ └── CMakeDirectoryInformation.cmake │ │ ├── wavelib │ │ │ ├── CMakeFiles │ │ │ │ ├── progress.make │ │ │ │ └── CMakeDirectoryInformation.cmake │ │ │ ├── src │ │ │ │ ├── CMakeFiles │ │ │ │ │ ├── progress.make │ │ │ │ │ ├── wavelib.dir │ │ │ │ │ │ ├── cmake_clean_target.cmake │ │ │ │ │ │ ├── cwt.c.o │ │ │ │ │ │ ├── conv.c.o │ │ │ │ │ │ ├── hsfft.c.o │ │ │ │ │ │ ├── real.c.o │ │ │ │ │ │ ├── cwtmath.c.o │ │ │ │ │ │ ├── wavefilt.c.o │ │ │ │ │ │ ├── wavefunc.c.o │ │ │ │ │ │ ├── wavelib.c.o │ │ │ │ │ │ ├── wtmath.c.o │ │ │ │ │ │ ├── progress.make │ │ │ │ │ │ ├── link.txt │ │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ │ ├── flags.make │ │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ │ ├── C.includecache │ │ │ │ │ │ └── depend.make │ │ │ │ │ └── CMakeDirectoryInformation.cmake │ │ │ │ └── cmake_install.cmake │ │ │ └── cmake_install.cmake │ │ ├── lib6mer.a │ │ ├── libutil.a │ │ ├── libwavelib.a │ │ ├── cmake_install.cmake │ │ └── Makefile │ ├── src │ │ ├── 6mer │ │ │ ├── CMakeFiles │ │ │ │ ├── progress.make │ │ │ │ ├── 6mer.dir │ │ │ │ │ ├── progress.make │ │ │ │ │ ├── cmake_clean_target.cmake │ │ │ │ │ ├── link.txt │ │ │ │ │ ├── 6mer_index.cpp.o │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ ├── depend.make │ │ │ │ │ ├── depend.internal │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ ├── CXX.includecache │ │ │ │ │ └── flags.make │ │ │ │ └── CMakeDirectoryInformation.cmake │ │ │ └── cmake_install.cmake │ │ ├── CMakeFiles │ │ │ ├── progress.make │ │ │ └── CMakeDirectoryInformation.cmake │ │ ├── util │ │ │ ├── CMakeFiles │ │ │ │ ├── progress.make │ │ │ │ ├── util.dir │ │ │ │ │ ├── progress.make │ │ │ │ │ ├── cmake_clean_target.cmake │ │ │ │ │ ├── qsort.cpp.o │ │ │ │ │ ├── exception.cpp.o │ │ │ │ │ ├── link.txt │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ ├── depend.make │ │ │ │ │ ├── depend.internal │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ ├── flags.make │ │ │ │ │ └── CXX.includecache │ │ │ │ └── CMakeDirectoryInformation.cmake │ │ │ └── cmake_install.cmake │ │ ├── mer2seq │ │ │ ├── CMakeFiles │ │ │ │ ├── progress.make │ │ │ │ ├── mer2seq.dir │ │ │ │ │ ├── progress.make │ │ │ │ │ ├── depend.make │ │ │ │ │ ├── link.txt │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ ├── flags.make │ │ │ │ │ └── DependInfo.cmake │ │ │ │ └── CMakeDirectoryInformation.cmake │ │ │ └── cmake_install.cmake │ │ ├── proc │ │ │ ├── CMakeFiles │ │ │ │ ├── progress.make │ │ │ │ ├── proc.dir │ │ │ │ │ ├── cmake_clean_target.cmake │ │ │ │ │ ├── progress.make │ │ │ │ │ ├── resample.cpp.o │ │ │ │ │ ├── link.txt │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ ├── flags.make │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ ├── depend.internal │ │ │ │ │ └── depend.make │ │ │ │ └── CMakeDirectoryInformation.cmake │ │ │ └── cmake_install.cmake │ │ ├── fastalign │ │ │ ├── CMakeFiles │ │ │ │ ├── progress.make │ │ │ │ ├── sat-align.dir │ │ │ │ │ ├── progress.make │ │ │ │ │ ├── depend.make │ │ │ │ │ ├── link.txt │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ ├── flags.make │ │ │ │ │ └── DependInfo.cmake │ │ │ │ └── CMakeDirectoryInformation.cmake │ │ │ └── cmake_install.cmake │ │ ├── fastquery │ │ │ ├── CMakeFiles │ │ │ │ ├── progress.make │ │ │ │ ├── sat-query.dir │ │ │ │ │ ├── progress.make │ │ │ │ │ ├── depend.make │ │ │ │ │ ├── link.txt │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ ├── flags.make │ │ │ │ │ └── DependInfo.cmake │ │ │ │ └── CMakeDirectoryInformation.cmake │ │ │ └── cmake_install.cmake │ │ ├── cmake_install.cmake │ │ └── Makefile │ └── cmake_install.cmake ├── lib │ ├── CMakeLists.txt │ ├── fast5 │ │ ├── CMakeLists.txt │ │ ├── src │ │ │ ├── .gitignore │ │ │ ├── .fast5_version.hpp.in │ │ │ ├── huffman-encode.cpp │ │ │ ├── huffman-decode.cpp │ │ │ ├── Makefile │ │ │ └── f5-mod.cpp │ │ └── include │ │ │ ├── fast5 │ │ │ ├── cwmap.fast5_ed_skip_1.inl │ │ │ ├── cwmap.fast5_ev_rel_skip_1.inl │ │ │ ├── cwmap.fast5_ev_move_1.inl │ │ │ ├── cwmap.fast5_fq_bp_1.inl │ │ │ ├── fast5_version.hpp │ │ │ ├── cwmap.fast5_fq_qv_1.inl │ │ │ ├── cwmap.fast5_ed_len_1.inl │ │ │ └── Bit_Packer.hpp │ │ │ └── CMakeLists.txt │ └── wavelib │ │ ├── unitTests │ │ ├── CMakeLists.txt │ │ └── wavelibBoostTests │ │ │ ├── BoostTest.cpp │ │ │ ├── BoostTest.h │ │ │ └── CMakeLists.txt │ │ ├── .gitignore │ │ ├── src │ │ ├── cwtmath.h │ │ ├── wavefunc.h │ │ ├── CMakeLists.txt │ │ ├── real.h │ │ ├── cwt.h │ │ ├── wavefilt.h │ │ ├── wtmath.h │ │ ├── conv.h │ │ ├── hsfft.h │ │ ├── real.c │ │ └── conv.c │ │ ├── test │ │ ├── wtreetest.c │ │ ├── dwpttest.c │ │ ├── modwttest.c │ │ ├── swttest.c │ │ ├── dwttest.c │ │ ├── signal.txt │ │ └── cwttest.c │ │ └── CMakeLists.txt ├── SATnano.kdev4 ├── src │ ├── tmp.zip │ ├── mer2seq │ │ ├── CMakeLists.txt │ │ ├── main.cpp │ │ └── opts.h │ ├── fastalign │ │ ├── CMakeLists.txt │ │ ├── main.cpp │ │ └── opts.h │ ├── fastquery │ │ └── CMakeLists.txt │ ├── CMakeLists.txt │ ├── util │ │ ├── exception.cpp │ │ ├── CMakeLists.txt │ │ ├── CMakeLists.txt~ │ │ ├── exception.cpp~ │ │ ├── qsort.h │ │ ├── qsort.h~ │ │ ├── exception.h~ │ │ └── exception.h │ ├── 6mer │ │ ├── CMakeLists.txt │ │ ├── 6mer_index.h │ │ └── 6mer_index.cpp │ └── proc │ │ ├── CMakeLists.txt │ │ ├── io.h │ │ └── proc.h ├── doc │ └── wavelib-doc.pdf ├── .kdev4 │ └── SATnano.kdev4 └── CMakeLists.txt ├── sat-query_centos6.5 ├── sat-query_fedora25 ├── sat-query_ubuntu14 ├── plot_nanofigure ├── util │ ├── seq2sig │ ├── NanoRaw_Label │ ├── Signal_Transform │ ├── genome_preprocess.py │ └── PlotSignal_SNP.py ├── README ├── source_code │ ├── Makefile │ └── NanoRaw_Label.cpp ├── example │ ├── refseq.fasta │ └── snpseq.fasta └── plot_figure.sh └── genome_subseq /SATnano/build/CMakeFiles/Progress/1: -------------------------------------------------------------------------------- 1 | empty -------------------------------------------------------------------------------- /SATnano/build/CMakeFiles/Progress/12: -------------------------------------------------------------------------------- 1 | empty -------------------------------------------------------------------------------- /SATnano/build/CMakeFiles/Progress/13: -------------------------------------------------------------------------------- 1 | empty -------------------------------------------------------------------------------- /SATnano/build/CMakeFiles/Progress/14: 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-o ../../bin/mer2seq -rdynamic ../../lib/lib6mer.a ../../lib/libproc.a -lm ../../lib/lib6mer.a ../../lib/libutil.a ../../lib/libwavelib.a -lhdf5 2 | -------------------------------------------------------------------------------- /SATnano/lib/fast5/include/fast5/fast5_version.hpp: -------------------------------------------------------------------------------- 1 | #ifndef __FAST5_VERSION_HPP 2 | #define __FAST5_VERSION_HPP 3 | 4 | namespace fast5 5 | { 6 | 7 | namespace 8 | { 9 | 10 | static char const * const version = "0.6.4"; 11 | 12 | } 13 | 14 | } 15 | 16 | #endif 17 | -------------------------------------------------------------------------------- /SATnano/lib/fast5/src/.fast5_version.hpp.in: -------------------------------------------------------------------------------- 1 | #ifndef __FAST5_VERSION_HPP 2 | #define __FAST5_VERSION_HPP 3 | 4 | namespace fast5 5 | { 6 | 7 | namespace 8 | { 9 | 10 | static char const * const version = "${VERSION}"; 11 | 12 | } 13 | 14 | } 15 | 16 | #endif 17 | -------------------------------------------------------------------------------- /SATnano/src/util/exception.cpp: -------------------------------------------------------------------------------- 1 | #include "exception.h" 2 | 3 | void ex::EX_THROW(const char* x) 4 | { 5 | std::ostringstream oss; 6 | oss << x; 7 | throw Exception(oss.str()); 8 | } -------------------------------------------------------------------------------- /SATnano/build/lib/wavelib/src/CMakeFiles/wavelib.dir/progress.make: -------------------------------------------------------------------------------- 1 | CMAKE_PROGRESS_1 = 1 2 | CMAKE_PROGRESS_2 = 2 3 | CMAKE_PROGRESS_3 = 3 4 | CMAKE_PROGRESS_4 = 4 5 | CMAKE_PROGRESS_5 = 5 6 | CMAKE_PROGRESS_6 = 6 7 | CMAKE_PROGRESS_7 = 7 8 | CMAKE_PROGRESS_8 = 8 9 | CMAKE_PROGRESS_9 = 9 10 | 11 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/unitTests/wavelibBoostTests/BoostTest.h: -------------------------------------------------------------------------------- 1 | 2 | 3 | #ifndef SWALLOWING_BOOSTTEST_H_ 4 | #define SWALLOWING_BOOSTTEST_H_ 5 | 6 | // we use the header only version of boost unit test 7 | #define BOOST_TEST_NO_LIB 8 | #include 9 | 10 | #endif // SWALLOWING_BOOSTTEST_H_ 11 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/.gitignore: -------------------------------------------------------------------------------- 1 | #Folders Ignore 2 | Bin/ 3 | Testing/ 4 | 5 | #cmake ignore 6 | CMakeCache.txt 7 | CMakeFiles/ 8 | CMakeScripts/ 9 | Makefile/ 10 | cmake_install.cmake 11 | install_manifest.txt 12 | 13 | #yml 14 | *.yml 15 | 16 | #Compiled 17 | *.a 18 | *.o 19 | *.lib 20 | *.so 21 | *.exe 22 | *.dll 23 | -------------------------------------------------------------------------------- /SATnano/src/6mer/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | aux_source_directory(. MER_SRCS) 3 | 4 | MESSAGE(STATUS "building 6mer") 5 | 6 | add_library (6mer STATIC ${MER_SRCS}) 7 | 8 | target_link_libraries(6mer) 9 | 10 | set_target_properties(6mer PROPERTIES OUTPUT_NAME "6mer") 11 | set_target_properties(6mer PROPERTIES CLEAN_DIRECT_OUTPUT 1) 12 | -------------------------------------------------------------------------------- /SATnano/build/src/6mer/CMakeFiles/6mer.dir/cmake_clean.cmake: -------------------------------------------------------------------------------- 1 | FILE(REMOVE_RECURSE 2 | "CMakeFiles/6mer.dir/6mer_index.cpp.o" 3 | "../../lib/lib6mer.a" 4 | ) 5 | 6 | # Per-language clean rules from dependency scanning. 7 | FOREACH(lang CXX) 8 | INCLUDE(CMakeFiles/6mer.dir/cmake_clean_${lang}.cmake OPTIONAL) 9 | ENDFOREACH(lang) 10 | -------------------------------------------------------------------------------- /SATnano/build/src/mer2seq/CMakeFiles/mer2seq.dir/cmake_clean.cmake: -------------------------------------------------------------------------------- 1 | FILE(REMOVE_RECURSE 2 | "CMakeFiles/mer2seq.dir/main.cpp.o" 3 | "../../bin/mer2seq.pdb" 4 | "../../bin/mer2seq" 5 | ) 6 | 7 | # Per-language clean rules from dependency scanning. 8 | FOREACH(lang CXX) 9 | INCLUDE(CMakeFiles/mer2seq.dir/cmake_clean_${lang}.cmake OPTIONAL) 10 | ENDFOREACH(lang) 11 | -------------------------------------------------------------------------------- /SATnano/build/src/util/CMakeFiles/util.dir/cmake_clean.cmake: -------------------------------------------------------------------------------- 1 | FILE(REMOVE_RECURSE 2 | "CMakeFiles/util.dir/qsort.cpp.o" 3 | "CMakeFiles/util.dir/exception.cpp.o" 4 | "../../lib/libutil.a" 5 | ) 6 | 7 | # Per-language clean rules from dependency scanning. 8 | FOREACH(lang CXX) 9 | INCLUDE(CMakeFiles/util.dir/cmake_clean_${lang}.cmake OPTIONAL) 10 | ENDFOREACH(lang) 11 | -------------------------------------------------------------------------------- /SATnano/build/src/fastalign/CMakeFiles/sat-align.dir/cmake_clean.cmake: -------------------------------------------------------------------------------- 1 | FILE(REMOVE_RECURSE 2 | "CMakeFiles/sat-align.dir/main.cpp.o" 3 | "../../bin/sat-align.pdb" 4 | "../../bin/sat-align" 5 | ) 6 | 7 | # Per-language clean rules from dependency scanning. 8 | FOREACH(lang CXX) 9 | INCLUDE(CMakeFiles/sat-align.dir/cmake_clean_${lang}.cmake OPTIONAL) 10 | ENDFOREACH(lang) 11 | -------------------------------------------------------------------------------- /SATnano/build/src/fastquery/CMakeFiles/sat-query.dir/cmake_clean.cmake: -------------------------------------------------------------------------------- 1 | FILE(REMOVE_RECURSE 2 | "CMakeFiles/sat-query.dir/main.cpp.o" 3 | "../../bin/sat-query.pdb" 4 | "../../bin/sat-query" 5 | ) 6 | 7 | # Per-language clean rules from dependency scanning. 8 | FOREACH(lang CXX) 9 | INCLUDE(CMakeFiles/sat-query.dir/cmake_clean_${lang}.cmake OPTIONAL) 10 | ENDFOREACH(lang) 11 | -------------------------------------------------------------------------------- /SATnano/build/src/6mer/CMakeFiles/6mer.dir/depend.make: -------------------------------------------------------------------------------- 1 | # CMAKE generated file: DO NOT EDIT! 2 | # Generated by "Unix Makefiles" Generator, CMake Version 2.6 3 | 4 | src/6mer/CMakeFiles/6mer.dir/6mer_index.cpp.o: ../src/6mer/6mer_index.cpp 5 | src/6mer/CMakeFiles/6mer.dir/6mer_index.cpp.o: ../src/6mer/6mer_index.h 6 | src/6mer/CMakeFiles/6mer.dir/6mer_index.cpp.o: ../src/6mer/6mer_index_official.rc 7 | 8 | -------------------------------------------------------------------------------- /SATnano/src/proc/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | aux_source_directory(. PROC_SRCS) 3 | 4 | MESSAGE(STATUS "building proc") 5 | 6 | include_directories(${PROJECT_SOURCE_DIR}) 7 | 8 | add_library (proc STATIC ${PROC_SRCS}) 9 | 10 | target_link_libraries(proc util wavelib m 6mer hdf5) # fftw3) 11 | 12 | set_target_properties(proc PROPERTIES OUTPUT_NAME "proc") 13 | set_target_properties(proc PROPERTIES CLEAN_DIRECT_OUTPUT 1) 14 | -------------------------------------------------------------------------------- /SATnano/src/util/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | #set(UTIL_SRCS exception.cpp dataf.cpp) 3 | aux_source_directory(. UTIL_SRCS) 4 | 5 | MESSAGE(STATUS "building util") 6 | 7 | include_directories(${PROJECT_SOURCE_DIR}) 8 | 9 | add_library(util STATIC ${UTIL_SRCS}) 10 | 11 | target_link_libraries(util) 12 | 13 | set_target_properties(util PROPERTIES OUTPUT_NAME "util") 14 | set_target_properties(util PROPERTIES CLEAN_DIRECT_OUTPUT 1) -------------------------------------------------------------------------------- /SATnano/build/lib/wavelib/src/CMakeFiles/wavelib.dir/link.txt: -------------------------------------------------------------------------------- 1 | /usr/bin/ar cr ../../libwavelib.a CMakeFiles/wavelib.dir/conv.c.o CMakeFiles/wavelib.dir/cwt.c.o CMakeFiles/wavelib.dir/cwtmath.c.o CMakeFiles/wavelib.dir/hsfft.c.o CMakeFiles/wavelib.dir/real.c.o CMakeFiles/wavelib.dir/wavefilt.c.o CMakeFiles/wavelib.dir/wavefunc.c.o CMakeFiles/wavelib.dir/wavelib.c.o CMakeFiles/wavelib.dir/wtmath.c.o 2 | /usr/bin/ranlib ../../libwavelib.a 3 | -------------------------------------------------------------------------------- /SATnano/lib/fast5/include/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | 3 | aux_source_directory(. FAST5_SRCS) 4 | 5 | MESSAGE(STATUS "building fast5") 6 | 7 | add_library (fast5 STATIC fast5.hpp ${FAST5_SRCS}) 8 | target_link_libraries(fast5 hdf5) 9 | 10 | set_target_properties(fast5 PROPERTIES LINKER_LANGUAGE Cxx) 11 | set_target_properties(fast5 PROPERTIES OUTPUT_NAME "fast5") 12 | set_target_properties(fast5 PROPERTIES CLEAN_DIRECT_OUTPUT 1) 13 | -------------------------------------------------------------------------------- /SATnano/src/util/CMakeLists.txt~: -------------------------------------------------------------------------------- 1 | 2 | #set(UTIL_SRCS exception.cpp dataf.cpp) 3 | aux_source_directory(. UTIL_SRCS) 4 | 5 | MESSAGE(STATUS "building util") 6 | 7 | include_directories(${PROJECT_SOURCE_DIR}) 8 | 9 | add_library (util STATIC ${UTIL_SRCS}) 10 | 11 | target_link_libraries(util sift) 12 | 13 | set_target_properties(util PROPERTIES OUTPUT_NAME "util") 14 | set_target_properties(util PROPERTIES CLEAN_DIRECT_OUTPUT 1) -------------------------------------------------------------------------------- /plot_nanofigure/source_code/Makefile: -------------------------------------------------------------------------------- 1 | 2 | 3 | # make the subdir first 4 | CXX = g++ 5 | #FLAG = -O3 -static 6 | FLAG = -O3 7 | SHELL :=/bin/bash 8 | 9 | all: 10 | # ------ all files -------# 11 | $(CXX) NanoRaw_Label.cpp $(FLAG) -o NanoRaw_Label 12 | $(CXX) Signal_Transform.cpp $(FLAG) -o Signal_Transform 13 | mkdir -p ../util 14 | mv NanoRaw_Label Signal_Transform ../util 15 | 16 | # clean all the temp files 17 | clean: 18 | -------------------------------------------------------------------------------- /SATnano/build/src/proc/CMakeFiles/proc.dir/cmake_clean.cmake: -------------------------------------------------------------------------------- 1 | FILE(REMOVE_RECURSE 2 | "CMakeFiles/proc.dir/proc.cpp.o" 3 | "CMakeFiles/proc.dir/base_fun.cpp.o" 4 | "CMakeFiles/proc.dir/resample.cpp.o" 5 | "CMakeFiles/proc.dir/io.cpp.o" 6 | "../../lib/libproc.a" 7 | ) 8 | 9 | # 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Targets to which this target links. 12 | SET(CMAKE_TARGET_LINKED_INFO_FILES 13 | ) 14 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/src/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | 2 | 3 | include_directories(${CMAKE_CURRENT_SOURCE_DIR}) 4 | 5 | set(SOURCE_FILES conv.c 6 | cwt.c 7 | cwtmath.c 8 | hsfft.c 9 | real.c 10 | wavefilt.c 11 | wavefunc.c 12 | wavelib.c 13 | wtmath.c 14 | ) 15 | 16 | set(HEADER_FILES conv.h 17 | cwt.h 18 | cwtmath.h 19 | hsfft.h 20 | real.h 21 | wavefilt.h 22 | wavefunc.h 23 | wavelib.h 24 | wtmath.h 25 | ) 26 | 27 | add_library(wavelib STATIC ${SOURCE_FILES} ${HEADER_FILES}) 28 | 29 | set_property(TARGET wavelib PROPERTY FOLDER "lib") 30 | 31 | -------------------------------------------------------------------------------- /SATnano/.kdev4/SATnano.kdev4: -------------------------------------------------------------------------------- 1 | [Buildset] 2 | BuildItems=@Variant(\x00\x00\x00\t\x00\x00\x00\x00\x01\x00\x00\x00\x0b\x00\x00\x00\x00\x01\x00\x00\x00\x0e\x00S\x00A\x00T\x00n\x00a\x00n\x00o) 3 | 4 | [CMake] 5 | Build Directory Count=1 6 | Current Build Directory Index=0 7 | ProjectRootRelative=./ 8 | 9 | [CMake][CMake Build Directory 0] 10 | Build Directory Path=file:///data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build 11 | Build Type=Debug 12 | CMake Binary=file:///usr/bin/cmake 13 | Environment Profile= 14 | Extra Arguments= 15 | Install Directory= 16 | 17 | [Defines And Includes][Compiler] 18 | Name=GCC 19 | Path=gcc 20 | Type=GCC 21 | 22 | [Project] 23 | VersionControlSupport=kdevgit 24 | -------------------------------------------------------------------------------- /SATnano/lib/fast5/include/fast5/cwmap.fast5_fq_qv_1.inl: -------------------------------------------------------------------------------- 1 | { "fast5_fq_qv_1", 2 | "10", "10", 3 | "16", "00000", 4 | "17", "00001", 5 | "18", "00010", 6 | "19", "00011", 7 | "20", "00100", 8 | "21", "00101", 9 | "22", "00110", 10 | "23", "00111", 11 | "24", "01000", 12 | "25", "01001", 13 | "26", "01010", 14 | "27", "01011", 15 | "28", "01100", 16 | "29", "01101", 17 | "30", "01110", 18 | "31", "01111", 19 | ".", "110000", 20 | "0", "110001", 21 | "1", "110010", 22 | "2", "110011", 23 | "3", "110100", 24 | "4", "110101", 25 | "5", "110110", 26 | "6", "110111", 27 | "7", "111000", 28 | "8", "111001", 29 | "9", "111010", 30 | "11", "111011", 31 | "12", "111100", 32 | "13", "111101", 33 | "14", "111110", 34 | "15", "111111", 35 | } 36 | -------------------------------------------------------------------------------- /SATnano/build/lib/wavelib/src/CMakeFiles/wavelib.dir/cmake_clean.cmake: -------------------------------------------------------------------------------- 1 | FILE(REMOVE_RECURSE 2 | "CMakeFiles/wavelib.dir/conv.c.o" 3 | "CMakeFiles/wavelib.dir/cwt.c.o" 4 | "CMakeFiles/wavelib.dir/cwtmath.c.o" 5 | "CMakeFiles/wavelib.dir/hsfft.c.o" 6 | "CMakeFiles/wavelib.dir/real.c.o" 7 | "CMakeFiles/wavelib.dir/wavefilt.c.o" 8 | "CMakeFiles/wavelib.dir/wavefunc.c.o" 9 | "CMakeFiles/wavelib.dir/wavelib.c.o" 10 | "CMakeFiles/wavelib.dir/wtmath.c.o" 11 | "../../libwavelib.pdb" 12 | "../../libwavelib.a" 13 | "../../libwavelib.so" 14 | ) 15 | 16 | # 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CMAKE generated file: DO NOT EDIT! 2 | # Generated by "Unix Makefiles" Generator, CMake Version 2.6 3 | 4 | # compile CXX with /usr/bin/c++ 5 | CXX_FLAGS = -std=c++0x -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/header -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/fast5/include -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/clapack_3.1/INCLUDE -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/clapack_3.1/BLAS/WRAP -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/cblas/INCLUDE -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/matrix 6 | 7 | CXX_DEFINES = 8 | 9 | -------------------------------------------------------------------------------- /SATnano/build/src/fastquery/CMakeFiles/sat-query.dir/flags.make: -------------------------------------------------------------------------------- 1 | # CMAKE generated file: DO NOT EDIT! 2 | # Generated by "Unix Makefiles" Generator, CMake Version 2.6 3 | 4 | # compile CXX with /usr/bin/c++ 5 | CXX_FLAGS = -std=c++0x -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/header -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/fast5/include -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/clapack_3.1/INCLUDE -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/clapack_3.1/BLAS/WRAP -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/cblas/INCLUDE -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/matrix 6 | 7 | CXX_DEFINES = 8 | 9 | -------------------------------------------------------------------------------- /SATnano/src/mer2seq/main.cpp: -------------------------------------------------------------------------------- 1 | #include "opts.h" 2 | #include 3 | #include 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include "util/exception.h" 11 | #include "6mer/6mer_index.h" 12 | 13 | int main(int argc, char **argv) 14 | { 15 | struct options opts; 16 | if(GetOpts(argc, argv, &opts) < 0){ 17 | return 0; 18 | } 19 | 20 | EX_TRACE("Transform genomes to signal sequence...\n"); 21 | 22 | std::vector genomes; 23 | std::vector signals; 24 | 25 | g::io::ReadATCG(opts.input, genomes); 26 | EX_TRACE("%ld genomes are readed.\n", genomes.size()); 27 | 28 | g::io::Genomes2SignalSequence(genomes, signals, 1); 29 | 30 | g::io::WriteSignalSequence("genome2sig.result", signals); 31 | 32 | // genome::Mer2Signal::FiveMer2Index("ATAAA"); 33 | 34 | return 0; 35 | } 36 | 37 | -------------------------------------------------------------------------------- /SATnano/build/src/proc/CMakeFiles/proc.dir/flags.make: -------------------------------------------------------------------------------- 1 | # CMAKE generated file: DO NOT EDIT! 2 | # Generated by "Unix Makefiles" Generator, CMake Version 2.6 3 | 4 | # compile CXX with /usr/bin/c++ 5 | CXX_FLAGS = -std=c++0x -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/header -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/fast5/include -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/clapack_3.1/INCLUDE -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/clapack_3.1/BLAS/WRAP -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/cblas/INCLUDE -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/matrix -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano 6 | 7 | CXX_DEFINES = 8 | 9 | -------------------------------------------------------------------------------- /SATnano/build/src/util/CMakeFiles/util.dir/flags.make: -------------------------------------------------------------------------------- 1 | # CMAKE generated file: DO NOT EDIT! 2 | # Generated by "Unix Makefiles" Generator, CMake Version 2.6 3 | 4 | # compile CXX with /usr/bin/c++ 5 | CXX_FLAGS = -std=c++0x -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/header -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/fast5/include -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/clapack_3.1/INCLUDE -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/clapack_3.1/BLAS/WRAP -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/cblas/INCLUDE -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/matrix -I/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano 6 | 7 | CXX_DEFINES = 8 | 9 | -------------------------------------------------------------------------------- /SATnano/src/6mer/6mer_index.h: -------------------------------------------------------------------------------- 1 | #ifndef FIVEMER_INDEX_H__ 2 | #define FIVEMER_INDEX_H__ 3 | 4 | #include 5 | #include 6 | 7 | #define KMER_NUM 4096 8 | #define TABLE_ITEMS 5 9 | 10 | namespace g{ 11 | 12 | class Mer2Signal 13 | { 14 | private: 15 | /* avg, var, len, #, #, #, # (defined in 5mer_index_table.rc) */ 16 | const static double index_table_6mer[KMER_NUM][TABLE_ITEMS]; 17 | // const static double index_table_6mer[4096]; 18 | 19 | public: 20 | static int SixMer2Index(const std::vector& sixmer); 21 | static int SixMer2Index(char g0, char g1, char g2, char g3, char g4, char g5); 22 | static int SixMer2Index(const std::string& sixmer); 23 | static int SixMer2Index(char const* sixmer); 24 | static double LevelMeanAt(int index); 25 | static double LevelStdvAt(int index); 26 | static double SdMeanAt(int index); 27 | static double SdStdvAt(int index); 28 | static double WeightAt(int index); 29 | }; 30 | 31 | 32 | } 33 | 34 | 35 | #endif -------------------------------------------------------------------------------- /plot_nanofigure/example/refseq.fasta: -------------------------------------------------------------------------------- 1 | >snp | 501 C -> A 2 | CTGATAAGTAATGGTGTATGCAGTGTTAGTTTTTACATAACCAGCAGTTGCTGTTTGGTCTGCGACGGCACGAACGTAAGACGCTTTAAAATCATAAACAGCAGATTTTGTCGTTGCATCCAGGGCTTTAGTATACACATCGCCAGGGTTGTTAATTTGAACCTGTTTGATAGTGGAACCATCAATATTGTGTAGAGCGATATTAACGCCGTCAGATGGGTTGTTAATAGACATGTCGTTGTTCAAAGTCCCTTTGCTGTTACCAAAGAAAACAGAACCGAAGGTCATTTTAGCCGTGCTACCTGGATTCGGATTTGCTTTGCTGCAGTCAACGGTGATGCTGAAAGGTTTAGCTTTAGCGCCAACGGTGTCATTCAGTACGCCAGCATCGATTTCACCAACGGTTGCGGTTTGCAGCAGGATCAGACCATCCTTGTTACCGCCGTCAACGCGGGTTTCACAGGTGTTATCAACAACCAGACCACTGATATTTAACTGACAGCCGTCCATATCAGCAGAAGCAGTACCTGCAACCATCGCCAGCATAAGACCAGACAGGGCAAAACCTAATTTTTTAGACATAAAAATCCTTTAATAAAATTCCATTAGTCAGACTACATGTTTGAAGAATGACTATTCATGACACAAATAGGAGAAACAAATGTTAGATATTAATGAGCAATGATATTTGTTACCCAAATTTACAACCATTGTTCATTAGGTCGCCTATTGTGCACTTTAGAAGCTTTTGAACAAATTAAATTTACTTAATTCAAAATTAAGTAAAAATAAGTTCACAAGTGCAATTGGTTAGGGTATGGAGATGGGATTGATATTTATTTATAGGAAGTTATATTATTTCCGCAAAGAGATGTTTAAACTAAAATCGTAATTAAGGAAAGAGATGAGATATGATTTTCAGAAAATATTTATATTCGCAATATAAATAAATTACCATTTGTTTAATTTGTCAAATGCTCTTGTATGTAAGATTTGACGC 3 | -------------------------------------------------------------------------------- /plot_nanofigure/example/snpseq.fasta: -------------------------------------------------------------------------------- 1 | >snp | 501 C -> A 2 | CTGATAAGTAATGGTGTATGCAGTGTTAGTTTTTACATAACCAGCAGTTGCTGTTTGGTCTGCGACGGCACGAACGTAAGACGCTTTAAAATCATAAACAGCAGATTTTGTCGTTGCATCCAGGGCTTTAGTATACACATCGCCAGGGTTGTTAATTTGAACCTGTTTGATAGTGGAACCATCAATATTGTGTAGAGCGATATTAACGCCGTCAGATGGGTTGTTAATAGACATGTCGTTGTTCAAAGTCCCTTTGCTGTTACCAAAGAAAACAGAACCGAAGGTCATTTTAGCCGTGCTACCTGGATTCGGATTTGCTTTGCTGCAGTCAACGGTGATGCTGAAAGGTTTAGCTTTAGCGCCAACGGTGTCATTCAGTACGCCAGCATCGATTTCACCAACGGTTGCGGTTTGCAGCAGGATCAGACCATCCTTGTTACCGCCGTCAACGCGGGTTTCACAGGTGTTATCAACAACCAGACCACTGATATTTAACTGACCGCCGTCCATATCAGCAGAAGCAGTACCTGCAACCATCGCCAGCATAAGACCAGACAGGGCAAAACCTAATTTTTTAGACATAAAAATCCTTTAATAAAATTCCATTAGTCAGACTACATGTTTGAAGAATGACTATTCATGACACAAATAGGAGAAACAAATGTTAGATATTAATGAGCAATGATATTTGTTACCCAAATTTACAACCATTGTTCATTAGGTCGCCTATTGTGCACTTTAGAAGCTTTTGAACAAATTAAATTTACTTAATTCAAAATTAAGTAAAAATAAGTTCACAAGTGCAATTGGTTAGGGTATGGAGATGGGATTGATATTTATTTATAGGAAGTTATATTATTTCCGCAAAGAGATGTTTAAACTAAAATCGTAATTAAGGAAAGAGATGAGATATGATTTTCAGAAAATATTTATATTCGCAATATAAATAAATTACCATTTGTTTAATTTGTCAAATGCTCTTGTATGTAAGATTTGACGC 3 | -------------------------------------------------------------------------------- /SATnano/build/lib/wavelib/src/CMakeFiles/wavelib.dir/flags.make: -------------------------------------------------------------------------------- 1 | # 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Save compiler ABI information. 27 | SET(CMAKE_C_SIZEOF_DATA_PTR "8") 28 | SET(CMAKE_C_COMPILER_ABI "ELF") 29 | 30 | IF(CMAKE_C_SIZEOF_DATA_PTR) 31 | SET(CMAKE_SIZEOF_VOID_P "${CMAKE_C_SIZEOF_DATA_PTR}") 32 | ENDIF(CMAKE_C_SIZEOF_DATA_PTR) 33 | 34 | IF(CMAKE_C_COMPILER_ABI) 35 | SET(CMAKE_INTERNAL_PLATFORM_ABI "${CMAKE_C_COMPILER_ABI}") 36 | ENDIF(CMAKE_C_COMPILER_ABI) 37 | -------------------------------------------------------------------------------- /genome_subseq: -------------------------------------------------------------------------------- 1 | #test 2 | AAACAAGGATGCATATATGAATGAACGATGCAGAGGCAATGCCGATGGCGATAGTGGGTATCATGTAGCCGCTTATGCTGGAAAGAAGCAATAACCCGCAGAAAAACAAAGCTCCAAGCTCAACAAAACTAAGGGCATAGACAATAACTACCGATGTCATATACCCATACTCTCTAATCTTGGCCAGTCGGCGCGTTCTGCTTCCGATTAGAAACGTCAAGGCAGCAATCAGGATTGCAATCATGGTTCCTGCATATGATGACAATGTCGCCCCAAGACCATCTCTATGAGCTGAAAAAGAAACACCAGGAATGTAGTGGCGGAAAAGGAGATAGCAAATGCTTACGATAACGTAAGGAATTATTACTATGTAAACACCAGGCATGATTCTGTTCCGCATAATTACTCCTGATAATTAATCCTTAACTTTGCCCACCTGCCTTTTAAAACATTCCAGTATATCACTTTTCATTCTTGCGTAGCAATATGCCATCTCTTCAGCTATCTCAGCATTGGTGACCTTGTTCAGAGGCGCTGAGAGATGGCCTTTTTCTGATAGATAATGTTCTGTTAAAATATCTCCGGCCTCATCTTTTGCCCGCAGGCTAATGTCTGAAAATTGAGGTGACGGGTTAAAAATAATATCCTTGGCAACCTTTTTATATCCCTTTTAAATTTTGGCTTAATGACTATATCCAATGAGTCAAAAAGCTCCCCTTCAATATCTGTTGCCCCTAAGACCTTTAATATATCGCCAAATACAGGTAGCTTGGCTTCTACCTTCACCGTTGTTCGGCCGATGAAATGCATATGCATAACATCGTCTTTGGTGGTTCCCCTCATCAGTGGCTCTATCTGAACGCGCTCTCCACTGCTTAATGACATTCCTTTCCCGATTAAAAATCTGTCAGATCGGATGTGGTCGGCCCGAAAACAGTTCTGGCAAAACCAATGGTGTCGCCTTCAACAAACAAAAAGATGGGAATCCCAATGATTCGTCATCTGCGAGGCTGTTCTTAATATCTTCAACTGAAGCTTTAGAGCGATTTATCTTCTGAACCAGACTCTTGTCATTTGTTTTGGTAAAGAGAAAAGTTTTTCCATCGATTTTATGAATATACAAATAATTGGAGCCAACCTGCAGGTGATGATTATCAGCCAGCAGAGAATTAA 3 | GGAAAACAGACAGGTTTATTGAGCGCTTATCTTTCCCTTTATTTTTGCTG 4 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/test/wtreetest.c: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include 4 | #include 5 | #include "../header/wavelib.h" 6 | 7 | int main() { 8 | int i, J, N, len; 9 | int X, Y; 10 | wave_object obj; 11 | wtree_object wt; 12 | double *inp, *oup; 13 | 14 | char *name = "db3"; 15 | obj = wave_init(name);// Initialize the wavelet 16 | N = 147; 17 | inp = (double*)malloc(sizeof(double)* N); 18 | for (i = 1; i < N + 1; ++i) { 19 | inp[i - 1] = -0.25*i*i*i + 25 * i *i + 10 * i; 20 | } 21 | J = 3; 22 | 23 | wt = wtree_init(obj, N, J);// Initialize the wavelet transform object 24 | setWTREEExtension(wt, "sym");// Options are "per" and "sym". Symmetric is the default option 25 | 26 | wtree(wt, inp); 27 | wtree_summary(wt); 28 | X = 3; 29 | Y = 5; 30 | len = getWTREENodelength(wt, X); 31 | printf("\n %d", len); 32 | printf("\n"); 33 | oup = (double*)malloc(sizeof(double)* len); 34 | 35 | printf("Node [%d %d] Coefficients : \n",X,Y); 36 | getWTREECoeffs(wt, X, Y, oup, len); 37 | for (i = 0; i < len; ++i) { 38 | printf("%g ", oup[i]); 39 | } 40 | printf("\n"); 41 | 42 | free(inp); 43 | free(oup); 44 | wave_free(obj); 45 | wtree_free(wt); 46 | return 0; 47 | } 48 | -------------------------------------------------------------------------------- /SATnano/build/CMakeFiles/CMakeDirectoryInformation.cmake: -------------------------------------------------------------------------------- 1 | # CMAKE generated file: DO NOT EDIT! 2 | # Generated by "Unix Makefiles" Generator, CMake Version 2.6 3 | 4 | # Relative path conversion top directories. 5 | SET(CMAKE_RELATIVE_PATH_TOP_SOURCE "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano") 6 | SET(CMAKE_RELATIVE_PATH_TOP_BINARY "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build") 7 | 8 | # 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Set the install configuration name. 10 | IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 11 | IF(BUILD_TYPE) 12 | STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" "" 13 | CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") 14 | ELSE(BUILD_TYPE) 15 | SET(CMAKE_INSTALL_CONFIG_NAME "") 16 | ENDIF(BUILD_TYPE) 17 | MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") 18 | ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 19 | 20 | # Set the component getting installed. 21 | IF(NOT CMAKE_INSTALL_COMPONENT) 22 | IF(COMPONENT) 23 | MESSAGE(STATUS "Install component: \"${COMPONENT}\"") 24 | SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}") 25 | ELSE(COMPONENT) 26 | SET(CMAKE_INSTALL_COMPONENT) 27 | ENDIF(COMPONENT) 28 | ENDIF(NOT CMAKE_INSTALL_COMPONENT) 29 | 30 | # Install shared libraries without execute permission? 31 | IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 32 | SET(CMAKE_INSTALL_SO_NO_EXE "0") 33 | ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 34 | 35 | -------------------------------------------------------------------------------- /SATnano/build/src/fastalign/cmake_install.cmake: -------------------------------------------------------------------------------- 1 | # Install script for directory: /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/fastalign 2 | 3 | # Set the install prefix 4 | IF(NOT DEFINED CMAKE_INSTALL_PREFIX) 5 | SET(CMAKE_INSTALL_PREFIX "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/bin") 6 | ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX) 7 | STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") 8 | 9 | # Set the install configuration name. 10 | IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 11 | IF(BUILD_TYPE) 12 | STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" "" 13 | CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") 14 | ELSE(BUILD_TYPE) 15 | SET(CMAKE_INSTALL_CONFIG_NAME "") 16 | ENDIF(BUILD_TYPE) 17 | MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") 18 | ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 19 | 20 | # Set the component getting installed. 21 | IF(NOT CMAKE_INSTALL_COMPONENT) 22 | IF(COMPONENT) 23 | MESSAGE(STATUS "Install component: \"${COMPONENT}\"") 24 | SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}") 25 | ELSE(COMPONENT) 26 | SET(CMAKE_INSTALL_COMPONENT) 27 | ENDIF(COMPONENT) 28 | ENDIF(NOT CMAKE_INSTALL_COMPONENT) 29 | 30 | # Install shared libraries without execute permission? 31 | IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 32 | SET(CMAKE_INSTALL_SO_NO_EXE "0") 33 | ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 34 | 35 | -------------------------------------------------------------------------------- /SATnano/build/src/fastquery/cmake_install.cmake: -------------------------------------------------------------------------------- 1 | # Install script for directory: /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/fastquery 2 | 3 | # Set the install prefix 4 | IF(NOT DEFINED CMAKE_INSTALL_PREFIX) 5 | SET(CMAKE_INSTALL_PREFIX "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/bin") 6 | ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX) 7 | STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") 8 | 9 | # Set the install configuration name. 10 | IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 11 | IF(BUILD_TYPE) 12 | STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" "" 13 | CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") 14 | ELSE(BUILD_TYPE) 15 | SET(CMAKE_INSTALL_CONFIG_NAME "") 16 | ENDIF(BUILD_TYPE) 17 | MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") 18 | ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 19 | 20 | # Set the component getting installed. 21 | IF(NOT CMAKE_INSTALL_COMPONENT) 22 | IF(COMPONENT) 23 | MESSAGE(STATUS "Install component: \"${COMPONENT}\"") 24 | SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}") 25 | ELSE(COMPONENT) 26 | SET(CMAKE_INSTALL_COMPONENT) 27 | ENDIF(COMPONENT) 28 | ENDIF(NOT CMAKE_INSTALL_COMPONENT) 29 | 30 | # Install shared libraries without execute permission? 31 | IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 32 | SET(CMAKE_INSTALL_SO_NO_EXE "0") 33 | ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 34 | 35 | -------------------------------------------------------------------------------- /SATnano/build/src/mer2seq/cmake_install.cmake: -------------------------------------------------------------------------------- 1 | # Install script for directory: /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/mer2seq 2 | 3 | # Set the install prefix 4 | IF(NOT DEFINED CMAKE_INSTALL_PREFIX) 5 | SET(CMAKE_INSTALL_PREFIX "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/bin") 6 | ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX) 7 | STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") 8 | 9 | # Set the install configuration name. 10 | IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 11 | IF(BUILD_TYPE) 12 | STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" "" 13 | CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") 14 | ELSE(BUILD_TYPE) 15 | SET(CMAKE_INSTALL_CONFIG_NAME "") 16 | ENDIF(BUILD_TYPE) 17 | MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") 18 | ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 19 | 20 | # Set the component getting installed. 21 | IF(NOT CMAKE_INSTALL_COMPONENT) 22 | IF(COMPONENT) 23 | MESSAGE(STATUS "Install component: \"${COMPONENT}\"") 24 | SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}") 25 | ELSE(COMPONENT) 26 | SET(CMAKE_INSTALL_COMPONENT) 27 | ENDIF(COMPONENT) 28 | ENDIF(NOT CMAKE_INSTALL_COMPONENT) 29 | 30 | # Install shared libraries without execute permission? 31 | IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 32 | SET(CMAKE_INSTALL_SO_NO_EXE "0") 33 | ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 34 | 35 | -------------------------------------------------------------------------------- /SATnano/build/lib/wavelib/src/cmake_install.cmake: -------------------------------------------------------------------------------- 1 | # Install script for directory: /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src 2 | 3 | # Set the install prefix 4 | IF(NOT DEFINED CMAKE_INSTALL_PREFIX) 5 | SET(CMAKE_INSTALL_PREFIX "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/bin") 6 | ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX) 7 | STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") 8 | 9 | # Set the install configuration name. 10 | IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 11 | IF(BUILD_TYPE) 12 | STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" "" 13 | CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") 14 | ELSE(BUILD_TYPE) 15 | SET(CMAKE_INSTALL_CONFIG_NAME "") 16 | ENDIF(BUILD_TYPE) 17 | MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") 18 | ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 19 | 20 | # Set the component getting installed. 21 | IF(NOT CMAKE_INSTALL_COMPONENT) 22 | IF(COMPONENT) 23 | MESSAGE(STATUS "Install component: \"${COMPONENT}\"") 24 | SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}") 25 | ELSE(COMPONENT) 26 | SET(CMAKE_INSTALL_COMPONENT) 27 | ENDIF(COMPONENT) 28 | ENDIF(NOT CMAKE_INSTALL_COMPONENT) 29 | 30 | # Install shared libraries without execute permission? 31 | IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 32 | SET(CMAKE_INSTALL_SO_NO_EXE "0") 33 | ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 34 | 35 | -------------------------------------------------------------------------------- /SATnano/lib/fast5/src/huffman-decode.cpp: -------------------------------------------------------------------------------- 1 | // 2 | // Part of: https://github.com/mateidavid/fast5 3 | // 4 | // Copyright (c) 2015-2017 Matei David, Ontario Institute for Cancer Research 5 | // MIT License 6 | // 7 | 8 | #include 9 | #include 10 | #include 11 | #include 12 | 13 | #include 14 | #include 15 | 16 | using namespace std; 17 | 18 | int main(int argc, char * argv[]) 19 | { 20 | logger::Logger::set_default_level(logger::level::debug); 21 | if (argc != 2) 22 | { 23 | cerr << "use: " << argv[0] << " " << endl; 24 | exit(EXIT_FAILURE); 25 | } 26 | string cw_fn = argv[1]; 27 | ifstream cw_f(cw_fn); 28 | fast5_pack::Huffman_Diff_Coder hc(cw_f, cw_fn); 29 | string l; 30 | map< string, string > cw_v_id; 31 | vector< uint8_t > cw_v; 32 | while (getline(cin, l)) 33 | { 34 | if (l[0] == '#') 35 | { 36 | istringstream iss(l.substr(1)); 37 | string tmp0; 38 | string tmp1; 39 | getline(iss, tmp0, '='); 40 | iss >> tmp1; 41 | cw_v_id[tmp0] = tmp1; 42 | } 43 | else 44 | { 45 | unsigned x; 46 | istringstream(l) >> x; 47 | cw_v.push_back(x); 48 | } 49 | } 50 | auto val_v = hc.decode(cw_v, cw_v_id); 51 | for (auto x : val_v) 52 | { 53 | cout << x << endl; 54 | } 55 | } 56 | -------------------------------------------------------------------------------- /SATnano/src/proc/io.h: -------------------------------------------------------------------------------- 1 | #ifndef IO_H__ 2 | #define IO_H__ 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include <6mer/6mer_index.h> 10 | #include "hdf5.h" 11 | 12 | namespace g{ 13 | namespace io{ 14 | 15 | bool ReadATCG(const char* name, std::vector& genomes); 16 | 17 | bool WriteATCG(const char* name, const std::vector& genomes); 18 | 19 | bool ReadSignalSequence(const char* name, std::vector& signals); 20 | 21 | bool WriteSignalSequence(const char* name, const std::vector& signals); 22 | 23 | void Genomes2SignalSequence(const std::vector& genomes, std::vector& signals, int scale = 1); 24 | 25 | void Genomes2SignalSequence(const std::vector& genomes, std::vector& level_means, std::vector& level_stdv, int scale = 1); 26 | 27 | void GetGenomeStdvInPositions(const std::vector& genomes, std::vector& level_stdv); 28 | 29 | std::string GetFileExtension(const std::string& filename); 30 | 31 | std::string GetFileName(const std::string& filename); 32 | 33 | bool GetFilesName(const char* dirname, std::vector& filenames); 34 | 35 | /** interface for fast5 data **/ 36 | bool ReadFast5ATCG(const char* name, std::vector& genomes); 37 | 38 | bool ReadFast5SignalSequence(const char* name, std::vector& signals); 39 | 40 | bool PrintFast5Info(const char* name); 41 | 42 | std::string GetFast5ID(const char* name); 43 | 44 | } 45 | 46 | } 47 | 48 | #endif 49 | -------------------------------------------------------------------------------- /SATnano/build/src/proc/CMakeFiles/proc.dir/DependInfo.cmake: -------------------------------------------------------------------------------- 1 | # The set of languages for which implicit dependencies are needed: 2 | SET(CMAKE_DEPENDS_LANGUAGES 3 | "CXX" 4 | ) 5 | # The set of files for implicit dependencies of each language: 6 | SET(CMAKE_DEPENDS_CHECK_CXX 7 | "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/base_fun.cpp" "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/proc/CMakeFiles/proc.dir/base_fun.cpp.o" 8 | "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/io.cpp" "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/proc/CMakeFiles/proc.dir/io.cpp.o" 9 | "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/proc.cpp" "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/proc/CMakeFiles/proc.dir/proc.cpp.o" 10 | "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/resample.cpp" "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/proc/CMakeFiles/proc.dir/resample.cpp.o" 11 | ) 12 | SET(CMAKE_CXX_COMPILER_ID "GNU") 13 | 14 | # Targets to which this target links. 15 | SET(CMAKE_TARGET_LINKED_INFO_FILES 16 | "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/util/CMakeFiles/util.dir/DependInfo.cmake" 17 | "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/lib/wavelib/src/CMakeFiles/wavelib.dir/DependInfo.cmake" 18 | "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/6mer/CMakeFiles/6mer.dir/DependInfo.cmake" 19 | ) 20 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/test/dwpttest.c: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include 4 | #include 5 | #include "../header/wavelib.h" 6 | 7 | double absmax(double *array, int N) { 8 | double max; 9 | int i; 10 | 11 | max = 0.0; 12 | for (i = 0; i < N; ++i) { 13 | if (fabs(array[i]) >= max) { 14 | max = fabs(array[i]); 15 | } 16 | } 17 | 18 | return max; 19 | } 20 | 21 | int main() { 22 | int i, J, N; 23 | wave_object obj; 24 | wpt_object wt; 25 | double *inp, *oup, *diff; 26 | 27 | char *name = "db4"; 28 | obj = wave_init(name);// Initialize the wavelet 29 | N = 788 + 23; 30 | inp = (double*)malloc(sizeof(double)* N); 31 | oup = (double*)malloc(sizeof(double)* N); 32 | diff = (double*)malloc(sizeof(double)* N); 33 | for (i = 1; i < N + 1; ++i) { 34 | //inp[i - 1] = -0.25*i*i*i + 25 * i *i + 10 * i; 35 | inp[i - 1] = i; 36 | } 37 | J = 4; 38 | 39 | wt = wpt_init(obj, N, J);// Initialize the wavelet transform Tree object 40 | setDWPTExtension(wt, "per");// Options are "per" and "sym". Symmetric is the default option 41 | setDWPTEntropy(wt, "logenergy", 0); 42 | 43 | dwpt(wt, inp); // Discrete Wavelet Packet Transform 44 | 45 | idwpt(wt, oup); // Inverse Discrete Wavelet Packet Transform 46 | 47 | for (i = 0; i < N; ++i) { 48 | diff[i] = (inp[i] - oup[i])/inp[i]; 49 | } 50 | 51 | wpt_summary(wt); // Tree Summary 52 | 53 | printf("\n MAX %g \n", absmax(diff, wt->siglength)); // If Reconstruction succeeded then the output should be a small value. 54 | 55 | free(inp); 56 | free(oup); 57 | free(diff); 58 | wave_free(obj); 59 | wpt_free(wt); 60 | return 0; 61 | } 62 | -------------------------------------------------------------------------------- /SATnano/src/util/qsort.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (c) 2008 Noah Snavely (snavely (at) cs.washington.edu) 3 | * and the University of Washington 4 | * 5 | * This program is free software; you can redistribute it and/or modify 6 | * it under the terms of the GNU General Public License as published by 7 | * the Free Software Foundation; either version 2 of the License, or 8 | * (at your option) any later version. 9 | * 10 | * This program is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 13 | * GNU General Public License for more details. 14 | * 15 | */ 16 | 17 | #ifndef __qsort_h__ 18 | #define __qsort_h__ 19 | 20 | 21 | /* Set whether we should sort in ascending or descending order */ 22 | void qsort_ascending(); 23 | void qsort_descending(); 24 | 25 | /* Sorts the array of doubles `arr' (of length n) and puts the 26 | * corresponding permutation in `perm' */ 27 | void qsort_perm(int n, double *arr, int *perm); 28 | 29 | /* Permute the array `arr' given permutation `perm' */ 30 | void permute_dbl(int n, double *arr, int *perm); 31 | void permute(int n, int size, void *arr, int *perm); 32 | 33 | /* Find the median in a set of doubles */ 34 | double median(int n, double *arr); 35 | double median_copy(int n, double *arr); 36 | 37 | /* Find the kth element in an unordered list of doubles (changes the 38 | * array) */ 39 | double kth_element(int n, int k, double *arr); 40 | /* Same as above, doesn't change the array */ 41 | double kth_element_copy(int n, int k, double *arr); 42 | 43 | #endif /* __qsort_h__ */ 44 | -------------------------------------------------------------------------------- /SATnano/build/lib/cmake_install.cmake: -------------------------------------------------------------------------------- 1 | # Install script for directory: /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib 2 | 3 | # Set the install prefix 4 | IF(NOT DEFINED CMAKE_INSTALL_PREFIX) 5 | SET(CMAKE_INSTALL_PREFIX "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/bin") 6 | ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX) 7 | STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") 8 | 9 | # Set the install configuration name. 10 | IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 11 | IF(BUILD_TYPE) 12 | STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" "" 13 | CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") 14 | ELSE(BUILD_TYPE) 15 | SET(CMAKE_INSTALL_CONFIG_NAME "") 16 | ENDIF(BUILD_TYPE) 17 | MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") 18 | ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 19 | 20 | # Set the component getting installed. 21 | IF(NOT CMAKE_INSTALL_COMPONENT) 22 | IF(COMPONENT) 23 | MESSAGE(STATUS "Install component: \"${COMPONENT}\"") 24 | SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}") 25 | ELSE(COMPONENT) 26 | SET(CMAKE_INSTALL_COMPONENT) 27 | ENDIF(COMPONENT) 28 | ENDIF(NOT CMAKE_INSTALL_COMPONENT) 29 | 30 | # Install shared libraries without execute permission? 31 | IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 32 | SET(CMAKE_INSTALL_SO_NO_EXE "0") 33 | ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 34 | 35 | IF(NOT CMAKE_INSTALL_LOCAL_ONLY) 36 | # Include the install script for each subdirectory. 37 | INCLUDE("/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/lib/wavelib/cmake_install.cmake") 38 | 39 | ENDIF(NOT CMAKE_INSTALL_LOCAL_ONLY) 40 | 41 | -------------------------------------------------------------------------------- /SATnano/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | project(SATnano) #Signal-level Analysis Toolkit for nanopore sequencing 2 | 3 | cmake_minimum_required(VERSION 2.6) 4 | 5 | include(CheckCXXCompilerFlag) 6 | CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11) 7 | CHECK_CXX_COMPILER_FLAG("-std=c++0x" COMPILER_SUPPORTS_CXX0X) 8 | if(COMPILER_SUPPORTS_CXX11) 9 | set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") 10 | elseif(COMPILER_SUPPORTS_CXX0X) 11 | set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x") 12 | else() 13 | message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no 14 | C++11 support. Please use a different C++ compiler.") 15 | endif() 16 | 17 | #the store of data in clapack or cblas is column main sequence 18 | 19 | set(WAVELET_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/lib/wavelib/header) 20 | set(FAST5_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/lib/fast5/include) 21 | #set(HDF5_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/lib/hdf5_1.8.16/src) 22 | set(CLAPACK_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/lib/clapack_3.1/INCLUDE) 23 | set(BLASWRAP_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/lib/clapack_3.1/BLAS/WRAP) 24 | set(CBLAS_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/lib/cblas/INCLUDE) 25 | set(MATRIX_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/lib/matrix) 26 | # set(STATS_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/lib/stats/include) 27 | 28 | include_directories(${PROJECT_SOURCE_DIR}/lib ${PROJECT_SOURCE_DIR}/src ${WAVELET_INCLUDE_DIR} ${HDF5_INCLUDE_DIR} 29 | ${FAST5_INCLUDE_DIR} ${CLAPACK_INCLUDE_DIR} ${BLASWRAP_INCLUDE_DIR} ${CBLAS_INCLUDE_DIR} ${MATRIX_INCLUDE_DIR}) 30 | 31 | set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin) 32 | set(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib) 33 | 34 | add_subdirectory(lib) 35 | add_subdirectory(src) 36 | -------------------------------------------------------------------------------- /SATnano/src/util/qsort.h~: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (c) 2008 Noah Snavely (snavely (at) cs.washington.edu) 3 | * and the University of Washington 4 | * 5 | * This program is free software; you can redistribute it and/or modify 6 | * it under the terms of the GNU General Public License as published by 7 | * the Free Software Foundation; either version 2 of the License, or 8 | * (at your option) any later version. 9 | * 10 | * This program is distributed in the hope that it will be useful, 11 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 13 | * GNU General Public License for more details. 14 | * 15 | */ 16 | 17 | #ifndef __qsort_h__ 18 | #define __qsort_h__ 19 | 20 | extern "C"{ 21 | 22 | /* Set whether we should sort in ascending or descending order */ 23 | void qsort_ascending(); 24 | void qsort_descending(); 25 | 26 | /* Sorts the array of doubles `arr' (of length n) and puts the 27 | * corresponding permutation in `perm' */ 28 | void qsort_perm(int n, double *arr, int *perm); 29 | 30 | /* Permute the array `arr' given permutation `perm' */ 31 | void permute_dbl(int n, double *arr, int *perm); 32 | void permute(int n, int size, void *arr, int *perm); 33 | 34 | /* Find the median in a set of doubles */ 35 | double median(int n, double *arr); 36 | double median_copy(int n, double *arr); 37 | 38 | /* Find the kth element in an unordered list of doubles (changes the 39 | * array) */ 40 | double kth_element(int n, int k, double *arr); 41 | /* Same as above, doesn't change the array */ 42 | double kth_element_copy(int n, int k, double *arr); 43 | 44 | } 45 | #endif /* __qsort_h__ */ 46 | -------------------------------------------------------------------------------- /SATnano/build/lib/wavelib/cmake_install.cmake: -------------------------------------------------------------------------------- 1 | # Install script for directory: /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib 2 | 3 | # Set the install prefix 4 | IF(NOT DEFINED CMAKE_INSTALL_PREFIX) 5 | SET(CMAKE_INSTALL_PREFIX "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/bin") 6 | ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX) 7 | STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") 8 | 9 | # Set the install configuration name. 10 | IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 11 | IF(BUILD_TYPE) 12 | STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" "" 13 | CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") 14 | ELSE(BUILD_TYPE) 15 | SET(CMAKE_INSTALL_CONFIG_NAME "") 16 | ENDIF(BUILD_TYPE) 17 | MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") 18 | ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 19 | 20 | # Set the component getting installed. 21 | IF(NOT CMAKE_INSTALL_COMPONENT) 22 | IF(COMPONENT) 23 | MESSAGE(STATUS "Install component: \"${COMPONENT}\"") 24 | SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}") 25 | ELSE(COMPONENT) 26 | SET(CMAKE_INSTALL_COMPONENT) 27 | ENDIF(COMPONENT) 28 | ENDIF(NOT CMAKE_INSTALL_COMPONENT) 29 | 30 | # Install shared libraries without execute permission? 31 | IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 32 | SET(CMAKE_INSTALL_SO_NO_EXE "0") 33 | ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 34 | 35 | IF(NOT CMAKE_INSTALL_LOCAL_ONLY) 36 | # Include the install script for each subdirectory. 37 | INCLUDE("/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/lib/wavelib/src/cmake_install.cmake") 38 | 39 | ENDIF(NOT CMAKE_INSTALL_LOCAL_ONLY) 40 | 41 | -------------------------------------------------------------------------------- /SATnano/src/6mer/6mer_index.cpp: -------------------------------------------------------------------------------- 1 | #include "6mer_index.h" 2 | #include 3 | 4 | #include "6mer_index_official.rc" 5 | #include 6 | 7 | /* A = 0; C = 1; G = 2; T = 3 */ 8 | int g::Mer2Signal::SixMer2Index(char const* sixmer) 9 | { 10 | // const short atag = 0, ctag = 1, gtag = 2, ttag = 3; 11 | short idx = 0; 12 | 13 | for(int i = 0; i < 6; i++){ 14 | short tag; 15 | switch(sixmer[i]){ 16 | case 'A': 17 | tag = 0; 18 | break; 19 | case 'C': 20 | tag = 1; 21 | break; 22 | case 'G': 23 | tag = 2; 24 | break; 25 | case 'T': 26 | tag = 3; 27 | break; 28 | } 29 | tag <<= (5-i)*2; 30 | idx |= tag; 31 | } 32 | 33 | return idx; 34 | } 35 | 36 | int g::Mer2Signal::SixMer2Index(char g0, char g1, char g2, char g3, char g4, char g5) 37 | { 38 | char tmp[6] = {g0, g1, g2, g3, g4, g5}; 39 | return SixMer2Index(tmp); 40 | } 41 | 42 | int g::Mer2Signal::SixMer2Index(const std::vector& sixmer) 43 | { 44 | return SixMer2Index(&(sixmer[0])); 45 | } 46 | 47 | int g::Mer2Signal::SixMer2Index(const std::string& sixmer) 48 | { 49 | return SixMer2Index(sixmer.c_str()); 50 | } 51 | 52 | double g::Mer2Signal::LevelMeanAt(int index) 53 | { 54 | return index_table_6mer[index][0]; 55 | // return index_table_6mer[index]; 56 | } 57 | 58 | double g::Mer2Signal::LevelStdvAt(int index) 59 | { 60 | return index_table_6mer[index][1]; 61 | } 62 | 63 | double g::Mer2Signal::SdMeanAt(int index) 64 | { 65 | return index_table_6mer[index][2]; 66 | } 67 | 68 | double g::Mer2Signal::SdStdvAt(int index) 69 | { 70 | return index_table_6mer[index][3]; 71 | } 72 | 73 | double g::Mer2Signal::WeightAt(int index) 74 | { 75 | return index_table_6mer[index][4]; 76 | } 77 | 78 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.6.0 FATAL_ERROR) 2 | 3 | set(PROJECT_NAME wavelib) 4 | project(${PROJECT_NAME} CXX C) 5 | 6 | 7 | # src root path 8 | set(WAVELIB_SRC_ROOT ${PROJECT_SOURCE_DIR} CACHE PATH "Wavelib source root") 9 | # binary output by default 10 | # set(COMMON_BIN_PATH ${CMAKE_BINARY_DIR}/Bin) 11 | # set(LIBRARY_OUTPUT_PATH ${COMMON_BIN_PATH}/${CMAKE_BUILD_TYPE}) 12 | # set(EXECUTABLE_OUTPUT_PATH ${COMMON_BIN_PATH}/${CMAKE_BUILD_TYPE}) 13 | # set where to find additional cmake modules if any 14 | set(CMAKE_MODULE_PATH ${WAVELIB_SRC_ROOT}/cmake ${CMAKE_MODULE_PATH}) 15 | 16 | 17 | set(WAVELIB_VERSION "1.0.0" CACHE STRING "Wavelib version" FORCE) 18 | # message(">>> Building Wavelib version: ${WAVELIB_VERSION}") 19 | # message(">>> EXECUTABLE_OUTPUT_PATH = ${EXECUTABLE_OUTPUT_PATH}") 20 | 21 | option(BUILD_UT "Enable Unit test" OFF) 22 | 23 | # cleanup prefix lib for Unix-like OSes 24 | set(CMAKE_SHARED_MODULE_PREFIX) 25 | 26 | # install target to this folder by default 27 | set(WAVELIB_BINARY_DIR ${WAVELIB_SRC_ROOT}/bin) 28 | if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) 29 | set(CMAKE_INSTALL_PREFIX "${WAVELIB_BINARY_DIR}" CACHE PATH "default install path" FORCE) 30 | endif() 31 | 32 | # make include globaly visible 33 | set(PROJECT_WIDE_INCLUDE ${WAVELIB_SRC_ROOT}/include) 34 | include_directories(${PROJECT_WIDE_INCLUDE}) 35 | 36 | 37 | 38 | 39 | include_directories(${COMMON_BIN_PATH}) 40 | 41 | if(BUILD_UT) 42 | include(CTest) 43 | enable_testing() 44 | add_subdirectory(unitTests) 45 | endif() 46 | 47 | add_subdirectory(src) 48 | 49 | #install(DIRECTORY ${WAVELIB_SRC_ROOT}/include/ DESTINATION include FILES_MATCHING PATTERN "*.h") 50 | -------------------------------------------------------------------------------- /plot_nanofigure/util/genome_preprocess.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import argparse 4 | import numpy as np 5 | import re 6 | 7 | 8 | #------------- functions ---------------# 9 | def load_genome(input_file): 10 | with open(input_file, 'r') as f: 11 | text = f.read() 12 | lines = text.splitlines() 13 | sequence = filter(lambda x: '>' not in x, lines) 14 | sequence = map(lambda x: x.strip(), sequence) 15 | sequence = ''.join(sequence) 16 | return sequence 17 | 18 | def save_genome(genome, output_file): 19 | with open(output_file, 'w') as f: 20 | f.write('>preprocess\n') 21 | f.write(genome+'\n') 22 | 23 | def replace_n(genome): 24 | n_index = [m.start() for m in re.finditer('N', genome)] 25 | genome_list = np.array([x for x in genome]) 26 | random_base = np.random.choice(['A','T','C','G'],len(n_index)) 27 | genome_list[n_index] = random_base 28 | genome = ''.join(genome_list) 29 | return genome 30 | 31 | 32 | #============== main =====================# 33 | if __name__ == '__main__': 34 | parser = argparse.ArgumentParser(description='pre-process input genome') 35 | 36 | #-> required arguments 37 | parser.add_argument('-i', action='store', dest='input', required=True, 38 | help='the input genome file in fasta format') 39 | parser.add_argument('-o', action='store', dest='output', required=True, 40 | help='prefix the output file') 41 | 42 | #-> optional arguments 43 | parser.add_argument('-r', action='store', dest='replace', 44 | default=False, type=bool, help='if we replace the ns or delete the ns') 45 | 46 | arg = parser.parse_args() 47 | genome = load_genome(arg.input) 48 | 49 | # deal with the not standard genome, containing 'N', or in lower case. 50 | genome = genome.upper() 51 | # replace all non ATCG nucleotides into 'N' 52 | genome = re.sub('[^ATCG]', 'N', genome) 53 | 54 | if arg.replace: 55 | genome = replace_n(genome) 56 | else: 57 | genome = genome.replace('N','') 58 | 59 | # output genome 60 | save_genome(genome, arg.output) 61 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/test/modwttest.c: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include 4 | #include 5 | #include "../header/wavelib.h" 6 | 7 | double absmax(double *array, int N) { 8 | double max; 9 | int i; 10 | 11 | max = 0.0; 12 | for (i = 0; i < N; ++i) { 13 | if (fabs(array[i]) >= max) { 14 | max = fabs(array[i]); 15 | } 16 | } 17 | 18 | return max; 19 | } 20 | 21 | int main() { 22 | wave_object obj; 23 | wt_object wt; 24 | double *inp, *out, *diff; 25 | int N, i, J; 26 | 27 | FILE *ifp; 28 | double temp[1200]; 29 | 30 | char *name = "db4"; 31 | obj = wave_init(name); 32 | wave_summary(obj); 33 | 34 | ifp = fopen("signal.txt", "r"); 35 | i = 0; 36 | if (!ifp) { 37 | printf("Cannot Open File"); 38 | exit(100); 39 | } 40 | while (!feof(ifp)) { 41 | fscanf(ifp, "%lf \n", &temp[i]); 42 | i++; 43 | } 44 | N = 177; 45 | 46 | inp = (double*)malloc(sizeof(double)* N); 47 | out = (double*)malloc(sizeof(double)* N); 48 | diff = (double*)malloc(sizeof(double)* N); 49 | //wmean = mean(temp, N); 50 | 51 | for (i = 0; i < N; ++i) { 52 | inp[i] = temp[i]; 53 | //printf("%g \n",inp[i]); 54 | } 55 | J = 2; 56 | 57 | wt = wt_init(obj, "modwt", N, J);// Initialize the wavelet transform object 58 | 59 | modwt(wt, inp);// Perform MODWT 60 | //MODWT output can be accessed using wt->output vector. Use wt_summary to find out how to extract appx and detail coefficients 61 | 62 | for (i = 0; i < wt->outlength; ++i) { 63 | printf("%g ",wt->output[i]); 64 | } 65 | 66 | imodwt(wt, out);// Perform ISWT (if needed) 67 | // Test Reconstruction 68 | 69 | 70 | for (i = 0; i < wt->siglength; ++i) { 71 | diff[i] = out[i] - inp[i]; 72 | } 73 | 74 | printf("\n MAX %g \n", absmax(diff, wt->siglength));// If Reconstruction succeeded then the output should be a small value. 75 | 76 | wt_summary(wt);// Prints the full summary. 77 | 78 | wave_free(obj); 79 | wt_free(wt); 80 | 81 | free(inp); 82 | free(out); 83 | free(diff); 84 | return 0; 85 | } 86 | 87 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/test/swttest.c: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include 4 | #include 5 | #include "../header/wavelib.h" 6 | 7 | double absmax(double *array, int N) { 8 | double max; 9 | int i; 10 | 11 | max = 0.0; 12 | for (i = 0; i < N; ++i) { 13 | if (fabs(array[i]) >= max) { 14 | max = fabs(array[i]); 15 | } 16 | } 17 | 18 | return max; 19 | } 20 | 21 | int main() { 22 | wave_object obj; 23 | wt_object wt; 24 | double *inp, *out, *diff; 25 | int N, i, J; 26 | 27 | FILE *ifp; 28 | double temp[1200]; 29 | 30 | char *name = "bior3.5"; 31 | obj = wave_init(name);// Initialize the wavelet 32 | 33 | ifp = fopen("signal.txt", "r"); 34 | i = 0; 35 | if (!ifp) { 36 | printf("Cannot Open File"); 37 | exit(100); 38 | } 39 | while (!feof(ifp)) { 40 | fscanf(ifp, "%lf \n", &temp[i]); 41 | i++; 42 | } 43 | N = 256; 44 | 45 | inp = (double*)malloc(sizeof(double)* N); 46 | out = (double*)malloc(sizeof(double)* N); 47 | diff = (double*)malloc(sizeof(double)* N); 48 | //wmean = mean(temp, N); 49 | 50 | for (i = 0; i < N; ++i) { 51 | inp[i] = temp[i]; 52 | //printf("%g \n",inp[i]); 53 | } 54 | J = 1; 55 | 56 | wt = wt_init(obj, "swt", N, J);// Initialize the wavelet transform object 57 | setWTConv(wt, "direct"); 58 | 59 | 60 | swt(wt, inp);// Perform SWT 61 | //SWT output can be accessed using wt->output vector. Use wt_summary to find out how to extract appx and detail coefficients 62 | 63 | for (i = 0; i < wt->outlength; ++i) { 64 | printf("%g ",wt->output[i]); 65 | } 66 | 67 | iswt(wt, out);// Perform ISWT (if needed) 68 | // Test Reconstruction 69 | 70 | 71 | for (i = 0; i < wt->siglength; ++i) { 72 | diff[i] = out[i] - inp[i]; 73 | } 74 | 75 | printf("\n MAX %g \n", absmax(diff, wt->siglength));// If Reconstruction succeeded then the output should be a small value. 76 | 77 | wt_summary(wt);// Prints the full summary. 78 | 79 | 80 | wave_free(obj); 81 | wt_free(wt); 82 | 83 | free(inp); 84 | free(out); 85 | free(diff); 86 | return 0; 87 | } 88 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/test/dwttest.c: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include 4 | #include 5 | #include "../header/wavelib.h" 6 | 7 | double absmax(double *array, int N) { 8 | double max; 9 | int i; 10 | 11 | max = 0.0; 12 | for (i = 0; i < N; ++i) { 13 | if (fabs(array[i]) >= max) { 14 | max = fabs(array[i]); 15 | } 16 | } 17 | 18 | return max; 19 | } 20 | 21 | int main() { 22 | wave_object obj; 23 | wt_object wt; 24 | double *inp,*out,*diff; 25 | int N, i,J; 26 | 27 | FILE *ifp; 28 | double temp[1200]; 29 | 30 | char *name = "db4"; 31 | obj = wave_init(name);// Initialize the wavelet 32 | 33 | ifp = fopen("signal.txt", "r"); 34 | i = 0; 35 | if (!ifp) { 36 | printf("Cannot Open File"); 37 | exit(100); 38 | } 39 | while (!feof(ifp)) { 40 | fscanf(ifp, "%lf \n", &temp[i]); 41 | i++; 42 | } 43 | N = 256; 44 | 45 | inp = (double*)malloc(sizeof(double)* N); 46 | out = (double*)malloc(sizeof(double)* N); 47 | diff = (double*)malloc(sizeof(double)* N); 48 | //wmean = mean(temp, N); 49 | 50 | for (i = 0; i < N; ++i) { 51 | inp[i] = temp[i]; 52 | //printf("%g \n",inp[i]); 53 | } 54 | J = 3; 55 | 56 | wt = wt_init(obj, "dwt", N, J);// Initialize the wavelet transform object 57 | setDWTExtension(wt, "sym");// Options are "per" and "sym". Symmetric is the default option 58 | setWTConv(wt, "direct"); 59 | 60 | dwt(wt, inp);// Perform DWT 61 | //DWT output can be accessed using wt->output vector. Use wt_summary to find out how to extract appx and detail coefficients 62 | 63 | for (i = 0; i < wt->outlength; ++i) { 64 | printf("%g ",wt->output[i]); 65 | } 66 | 67 | idwt(wt, out);// Perform IDWT (if needed) 68 | // Test Reconstruction 69 | for (i = 0; i < wt->siglength; ++i) { 70 | diff[i] = out[i] - inp[i]; 71 | } 72 | 73 | printf("\n MAX %g \n", absmax(diff, wt->siglength)); // If Reconstruction succeeded then the output should be a small value. 74 | 75 | wt_summary(wt);// Prints the full summary. 76 | wave_free(obj); 77 | wt_free(wt); 78 | 79 | free(inp); 80 | free(out); 81 | free(diff); 82 | return 0; 83 | } 84 | -------------------------------------------------------------------------------- /SATnano/build/src/proc/CMakeFiles/proc.dir/depend.internal: -------------------------------------------------------------------------------- 1 | # CMAKE generated file: DO NOT EDIT! 2 | # Generated by "Unix Makefiles" Generator, CMake Version 2.6 3 | 4 | src/proc/CMakeFiles/proc.dir/base_fun.cpp.o 5 | ../lib/wavelib/header/wavelib.h 6 | ../src/6mer/6mer_index.h 7 | ../src/util/exception.h 8 | ../src/util/qsort.h 9 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/base_fun.cpp 10 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/io.h 11 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/proc.h 12 | src/proc/CMakeFiles/proc.dir/io.cpp.o 13 | ../lib/fast5/include/fast5.hpp 14 | ../lib/fast5/include/fast5/Bit_Packer.hpp 15 | ../lib/fast5/include/fast5/Huffman_Packer.hpp 16 | ../lib/fast5/include/fast5/cwmap.fast5_ed_len_1.inl 17 | ../lib/fast5/include/fast5/cwmap.fast5_ed_skip_1.inl 18 | ../lib/fast5/include/fast5/cwmap.fast5_ev_move_1.inl 19 | ../lib/fast5/include/fast5/cwmap.fast5_ev_rel_skip_1.inl 20 | ../lib/fast5/include/fast5/cwmap.fast5_fq_bp_1.inl 21 | ../lib/fast5/include/fast5/cwmap.fast5_fq_qv_1.inl 22 | ../lib/fast5/include/fast5/cwmap.fast5_rw_1.inl 23 | ../lib/fast5/include/fast5/fast5_version.hpp 24 | ../lib/fast5/include/fast5/hdf5_tools.hpp 25 | ../lib/fast5/include/fast5/logger.hpp 26 | ../src/6mer/6mer_index.h 27 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/io.cpp 28 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/io.h 29 | src/proc/CMakeFiles/proc.dir/proc.cpp.o 30 | ../lib/wavelib/header/wavelib.h 31 | ../src/6mer/6mer_index.h 32 | ../src/util/exception.h 33 | ../src/util/qsort.h 34 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/base_fun.cpp 35 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/io.h 36 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/proc.cpp 37 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/proc.h 38 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/resample.cpp 39 | src/proc/CMakeFiles/proc.dir/resample.cpp.o 40 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src/proc/resample.cpp 41 | -------------------------------------------------------------------------------- /SATnano/src/mer2seq/opts.h: -------------------------------------------------------------------------------- 1 | #ifndef OPTS_H__ 2 | #define OPTS_H__ 3 | 4 | #include 5 | #include 6 | #include 7 | extern "C" { 8 | #include 9 | } 10 | #include "util/exception.h" 11 | 12 | struct options { 13 | char input[255]; 14 | char output[255]; 15 | }; 16 | 17 | inline int GetOpts(int argc, char **argv, options* opts_){ 18 | 19 | static struct option longopts[] = { 20 | { "help", no_argument, NULL, 'h' }, 21 | { "output", required_argument, NULL, 'o' }, 22 | { "input", required_argument, NULL, 'i' }, 23 | { NULL, 0, NULL, 0 } 24 | }; 25 | 26 | if((argc != 5) && argc >= 3 || (argc == 2 && argv[1][0] != '-' && argv[1][1] != 'h') || argc == 1){ 27 | EX_TRACE("[-i GENOME FILE][-o SEQUENCE FILE]\n"); 28 | return -1; 29 | } 30 | 31 | int ch; 32 | while((ch = getopt_long(argc, argv, "hi:o:", longopts, NULL))!= -1){ 33 | switch (ch) { 34 | 35 | case '?': 36 | EX_TRACE("Invalid option '%s'.", argv[optind-1]); 37 | return -1; 38 | 39 | case ':': 40 | EX_TRACE("Missing option argument for '%s'.", argv[optind-1]); 41 | return -1; 42 | 43 | case 'h': 44 | EX_TRACE("[-i GENOME FILE][-o SEQUENCE FILE]\n"); 45 | return 0; 46 | 47 | case 'i': 48 | { 49 | std::istringstream iss(optarg); 50 | iss >> opts_->input; 51 | if (iss.fail()){ 52 | EX_TRACE("Invalid argument '%s'.", optarg); 53 | return -1; 54 | } 55 | } 56 | break; 57 | 58 | case 'o': 59 | { 60 | std::istringstream iss(optarg); 61 | iss >> opts_->output; 62 | if (iss.fail()){ 63 | EX_TRACE("Invalid argument '%s'.", optarg); 64 | return -1; 65 | } 66 | } 67 | break; 68 | 69 | case 0: 70 | break; 71 | 72 | default: 73 | assert(false); 74 | } 75 | } 76 | return 1; 77 | } 78 | 79 | #endif 80 | -------------------------------------------------------------------------------- /SATnano/build/src/cmake_install.cmake: -------------------------------------------------------------------------------- 1 | # Install script for directory: /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/src 2 | 3 | # Set the install prefix 4 | IF(NOT DEFINED CMAKE_INSTALL_PREFIX) 5 | SET(CMAKE_INSTALL_PREFIX "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/bin") 6 | ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX) 7 | STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") 8 | 9 | # Set the install configuration name. 10 | IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 11 | IF(BUILD_TYPE) 12 | STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" "" 13 | CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") 14 | ELSE(BUILD_TYPE) 15 | SET(CMAKE_INSTALL_CONFIG_NAME "") 16 | ENDIF(BUILD_TYPE) 17 | MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") 18 | ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 19 | 20 | # Set the component getting installed. 21 | IF(NOT CMAKE_INSTALL_COMPONENT) 22 | IF(COMPONENT) 23 | MESSAGE(STATUS "Install component: \"${COMPONENT}\"") 24 | SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}") 25 | ELSE(COMPONENT) 26 | SET(CMAKE_INSTALL_COMPONENT) 27 | ENDIF(COMPONENT) 28 | ENDIF(NOT CMAKE_INSTALL_COMPONENT) 29 | 30 | # Install shared libraries without execute permission? 31 | IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 32 | SET(CMAKE_INSTALL_SO_NO_EXE "0") 33 | ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) 34 | 35 | IF(NOT CMAKE_INSTALL_LOCAL_ONLY) 36 | # Include the install script for each subdirectory. 37 | INCLUDE("/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/fastquery/cmake_install.cmake") 38 | INCLUDE("/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/fastalign/cmake_install.cmake") 39 | INCLUDE("/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/util/cmake_install.cmake") 40 | INCLUDE("/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/6mer/cmake_install.cmake") 41 | INCLUDE("/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/mer2seq/cmake_install.cmake") 42 | INCLUDE("/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build/src/proc/cmake_install.cmake") 43 | 44 | ENDIF(NOT CMAKE_INSTALL_LOCAL_ONLY) 45 | 46 | -------------------------------------------------------------------------------- /SATnano/build/cmake_install.cmake: -------------------------------------------------------------------------------- 1 | # Install script for directory: /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano 2 | 3 | # Set the install prefix 4 | IF(NOT DEFINED CMAKE_INSTALL_PREFIX) 5 | SET(CMAKE_INSTALL_PREFIX "/mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/bin") 6 | ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX) 7 | STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX 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.DELETE_ON_ERROR: 12 | .PHONY: all help list clean check_hdf5 13 | 14 | HDF5_DIR ?= /usr/local 15 | HDF5_INCLUDE_DIR ?= ${HDF5_DIR}/include 16 | HDF5_LIB_DIR ?= ${HDF5_DIR}/lib 17 | HDF5_LIB ?= hdf5 18 | TCLAP_DIR ?= tclap 19 | HPPTOOLS_DIR ?= hpptools 20 | FAST5_DIR ?= ${CURDIR}/../include 21 | 22 | TARGETS = f5ls f5ls-full hdf5-mod f5-mod 23 | EXTRA_TARGETS = f5dump f5pack 24 | HPP_FILES := $(addprefix ${FAST5_DIR}/, fast5.hpp fast5/hdf5_tools.hpp fast5/Huffman_Packer.hpp fast5/Bit_Packer.hpp) 25 | 26 | CXXFLAGS := -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic 27 | CPPFLAGS := -isystem ${HDF5_INCLUDE_DIR} -I $(FAST5_DIR) 28 | EXTRA_CPPFLAGS := -isystem ${TCLAP_DIR}/include -I ${HPPTOOLS_DIR}/include 29 | LDFLAGS := -L${HDF5_LIB_DIR} -Wl,--rpath=${HDF5_LIB_DIR} -l${HDF5_LIB} -lpthread -lz -ldl 30 | 31 | default: ${TARGETS} 32 | 33 | all: default ${EXTRA_TARGETS} 34 | 35 | print-%: 36 | @echo '$*=$($*)' 37 | 38 | help: ## This help. 39 | @awk 'BEGIN {FS = ":.*?## "} /^[a-zA-Z_-]+:.*?## / {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' $(MAKEFILE_LIST) 40 | 41 | list: 42 | @echo "TARGETS=${TARGETS}" 43 | 44 | clean: 45 | rm -rf ${TARGETS} ${EXTRA_TARGETS} 46 | 47 | check_hdf5: 48 | @[ -f "${HDF5_INCLUDE_DIR}/H5pubconf.h" ] || { echo "HDF5 headers not found" >&2; exit 1; } 49 | @[ -f "${HDF5_LIB_DIR}/lib${HDF5_LIB}.so" ] || [ -f "${HDF5_LIB_DIR}/lib${HDF5_LIB}.a" ] || { echo "HDF5 library not found" >&2; exit 1; } 50 | 51 | check_tclap: 52 | @[ -f "${TCLAP_DIR}/include/tclap/CmdLine.h" ] || { echo "TCLAP not found; get it from https://github.com/mateidavid/tclap.git" >&2; exit 1; } 53 | 54 | check_hpptools: 55 | @[ -f "${HPPTOOLS_DIR}/include/alg.hpp" ] || { echo "HPPTOOLS not found; get it from https://github.com/mateidavid/hpptools.git" >&2; exit 1; } 56 | 57 | %: %.cpp ${HPP_FILES} | check_hdf5 58 | ${CXX} ${CXXFLAGS} ${CPPFLAGS} -o $@ $< ${LDFLAGS} 59 | 60 | f5dump: f5dump.cpp ${HPP_FILES} | check_hdf5 check_tclap 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-18.6741 -18.6741 -18.6741 -18.6741 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 6.3259 34.8066 34.6752 34.5285 34.3645 34.1812 33.9763 33.7474 33.4917 33.2058 32.8863 32.5294 32.1304 31.6846 31.1864 30.6296 30.0074 29.3121 28.5350 27.6667 26.6963 25.6118 24.3999 23.0456 21.5322 19.8408 17.9507 15.8385 13.4781 10.8403 7.8925 4.5982 0.9168 -3.1972 -7.7947 -12.9325 -18.6741 -18.6741 -18.6741 -18.6741 -18.6741 -18.6741 -18.6741 -18.6741 -18.6741 -18.6741 -18.6741 -18.6741 -18.6741 -18.6741 -18.3237 -------------------------------------------------------------------------------- /SATnano/lib/wavelib/test/cwttest.c: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include 4 | #include 5 | #include "../header/wavelib.h" 6 | 7 | int main() { 8 | int i, N, J,subscale,a0,iter,nd,k; 9 | double *inp,*oup; 10 | double dt, dj,s0, param,mn; 11 | double td,tn,den, num, recon_mean, recon_var; 12 | cwt_object wt; 13 | 14 | FILE *ifp; 15 | double temp[1200]; 16 | 17 | char *wave = "morlet";// Set Morlet wavelet. Other options "paul" and "dog" 18 | char *type = "pow"; 19 | 20 | N = 504; 21 | param = 6.0; 22 | subscale = 4; 23 | dt = 0.25; 24 | s0 = dt; 25 | dj = 1.0 / (double)subscale; 26 | J = 11 * subscale; // Total Number of scales 27 | a0 = 2;//power 28 | 29 | ifp = fopen("sst_nino3.dat", "r"); 30 | i = 0; 31 | if (!ifp) { 32 | printf("Cannot Open File"); 33 | exit(100); 34 | } 35 | while (!feof(ifp)) { 36 | fscanf(ifp, "%lf \n", &temp[i]); 37 | i++; 38 | } 39 | 40 | fclose(ifp); 41 | 42 | wt = cwt_init(wave, param, N,dt, J); 43 | 44 | inp = (double*)malloc(sizeof(double)* N); 45 | oup = (double*)malloc(sizeof(double)* N); 46 | 47 | for (i = 0; i < N; ++i) { 48 | inp[i] = temp[i] ; 49 | } 50 | 51 | setCWTScales(wt, s0, dj, type, a0); 52 | 53 | cwt(wt, inp); 54 | 55 | printf("\n MEAN %g \n", wt->smean); 56 | 57 | mn = 0.0; 58 | 59 | for (i = 0; i < N; ++i) { 60 | mn += sqrt(wt->output[i].re * wt->output[i].re + wt->output[i].im * wt->output[i].im); 61 | } 62 | 63 | cwt_summary(wt); 64 | 65 | printf("\n abs mean %g \n", mn / N); 66 | 67 | printf("\n\n"); 68 | printf("Let CWT w = w(j, n/2 - 1) where n = %d\n\n", N); 69 | nd = N/2 - 1; 70 | 71 | printf("%-15s%-15s%-15s%-15s \n","j","Scale","Period","ABS(w)^2"); 72 | for(k = 0; k < wt->J;++k) { 73 | iter = nd + k * N; 74 | printf("%-15d%-15lf%-15lf%-15lf \n",k,wt->scale[k],wt->period[k], 75 | wt->output[iter].re * wt->output[iter].re + wt->output[iter].im * wt->output[iter].im); 76 | } 77 | 78 | icwt(wt, oup); 79 | 80 | num = den = recon_var = recon_mean = 0.0; 81 | printf("\n\n"); 82 | printf("Signal Reconstruction\n"); 83 | printf("%-15s%-15s%-15s \n","i","Input(i)","Output(i)"); 84 | 85 | for (i = N - 10; i < N; ++i) { 86 | printf("%-15d%-15lf%-15lf \n", i,inp[i] , oup[i]); 87 | } 88 | 89 | for (i = 0; i < N; ++i) { 90 | //printf("%g %g \n", oup[i] ,inp[i] - wt->smean); 91 | td = inp[i] ; 92 | tn = oup[i] - td; 93 | num += (tn * tn); 94 | den += (td * td); 95 | recon_mean += oup[i]; 96 | } 97 | 98 | recon_var = sqrt(num / N); 99 | recon_mean /= N; 100 | 101 | printf("\nRMS Error %g \n", sqrt(num) / sqrt(den)); 102 | printf("\nVariance %g \n", recon_var); 103 | printf("\nMean %g \n", recon_mean); 104 | 105 | free(inp); 106 | free(oup); 107 | cwt_free(wt); 108 | return 0; 109 | } 110 | -------------------------------------------------------------------------------- /SATnano/lib/fast5/include/fast5/cwmap.fast5_ed_len_1.inl: -------------------------------------------------------------------------------- 1 | { "fast5_ed_len_1", 2 | "8", "001", 3 | "7", "010", 4 | "6", "100", 5 | "5", "111", 6 | "12", "0001", 7 | "11", "1010", 8 | "10", "1100", 9 | "9", "1101", 10 | "16", "00001", 11 | "4", "01101", 12 | "15", "01110", 13 | "14", "10110", 14 | "13", "10111", 15 | "19", "000001", 16 | "18", "011001", 17 | "17", "011111", 18 | "22", "0110000", 19 | "21", "0111100", 20 | "20", "0111101", 21 | "25", "00000010", 22 | "24", "01100010", 23 | "23", "01100011", 24 | "28", "000000001", 25 | "27", "000000110", 26 | "26", "000000111", 27 | "31", "0000000000", 28 | "30", "0000000100", 29 | "29", "0000000111", 30 | "32", "00000001010", 31 | "34", "000000000100", 32 | "35", "000000000110", 33 | "33", "000000011011", 34 | "41", "0000000001011", 35 | "40", "0000000001110", 36 | "36", "0000000101100", 37 | "37", "0000000110100", 38 | "38", "00000000010101", 39 | "42", "00000000011110", 40 | "39", "00000001101011", 41 | "99", "000000000101000", 42 | "100", "000000000101001", 43 | "43", "000000000111110", 44 | "44", "000000000111111", 45 | "46", "000000010110100", 46 | "53", "000000010110101", 47 | ".", "0000000101101100", 48 | "1", "0000000101101101", 49 | "2", "0000000101101110", 50 | "3", "0000000101101111", 51 | "45", "0000000101110000", 52 | "47", "0000000101110001", 53 | "48", "0000000101110010", 54 | "49", "0000000101110011", 55 | "50", "0000000101110100", 56 | "51", "0000000101110101", 57 | "52", "0000000101110110", 58 | "54", "0000000101110111", 59 | "55", "0000000101111000", 60 | "56", "0000000101111001", 61 | "57", "0000000101111010", 62 | "58", "0000000101111011", 63 | "59", "0000000101111100", 64 | "60", "0000000101111101", 65 | "61", "0000000101111110", 66 | "62", "0000000101111111", 67 | "63", "0000000110000000", 68 | "64", "0000000110000001", 69 | "65", "0000000110000010", 70 | "66", "0000000110000011", 71 | "67", "0000000110000100", 72 | "68", "0000000110000101", 73 | "69", "0000000110000110", 74 | "70", "0000000110000111", 75 | "71", "0000000110001000", 76 | "72", "0000000110001001", 77 | "73", "0000000110001010", 78 | "74", "0000000110001011", 79 | "75", "0000000110001100", 80 | "76", "0000000110001101", 81 | "77", "0000000110001110", 82 | "78", "0000000110001111", 83 | "79", "0000000110010000", 84 | "80", "0000000110010001", 85 | "81", "0000000110010010", 86 | "82", "0000000110010011", 87 | "83", "0000000110010100", 88 | "84", "0000000110010101", 89 | "85", "0000000110010110", 90 | "86", "0000000110010111", 91 | "87", "0000000110011000", 92 | "88", "0000000110011001", 93 | "89", "0000000110011010", 94 | "90", "0000000110011011", 95 | "91", "0000000110011100", 96 | "92", "0000000110011101", 97 | "93", "0000000110011110", 98 | "94", "0000000110011111", 99 | "95", "0000000110101000", 100 | "96", "0000000110101001", 101 | "97", "0000000110101010", 102 | "98", "0000000110101011", 103 | } 104 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/src/real.c: -------------------------------------------------------------------------------- 1 | /* 2 | * real.c 3 | * 4 | * Created on: Apr 20, 2013 5 | * Author: Rafat Hussain 6 | */ 7 | #include 8 | #include "real.h" 9 | 10 | fft_real_object fft_real_init(int N, int sgn) { 11 | fft_real_object obj = NULL; 12 | fft_type PI, theta; 13 | int k; 14 | 15 | PI = 3.1415926535897932384626433832795; 16 | 17 | obj = (fft_real_object) malloc (sizeof(struct fft_real_set) + sizeof(fft_data)* (N/2)); 18 | 19 | obj->cobj = fft_init(N/2,sgn); 20 | 21 | for (k = 0; k < N/2;++k) { 22 | theta = PI2*k/N; 23 | obj->twiddle2[k].re = cos(theta); 24 | obj->twiddle2[k].im = sin(theta); 25 | 26 | } 27 | 28 | 29 | return obj; 30 | 31 | 32 | } 33 | 34 | void fft_r2c_exec(fft_real_object obj,fft_type *inp,fft_data *oup) { 35 | fft_data* cinp; 36 | fft_data* coup; 37 | int i,N2,N; 38 | fft_type temp1,temp2; 39 | N2 = obj->cobj->N; 40 | N = N2*2; 41 | 42 | cinp = (fft_data*) malloc (sizeof(fft_data) * N2); 43 | coup = (fft_data*) malloc (sizeof(fft_data) * N2); 44 | 45 | for (i = 0; i < N2; ++i) { 46 | cinp[i].re = inp[2*i]; 47 | cinp[i].im = inp[2*i+1]; 48 | } 49 | 50 | fft_exec(obj->cobj,cinp,coup); 51 | 52 | oup[0].re = coup[0].re + coup[0].im; 53 | oup[0].im = 0.0; 54 | 55 | for (i = 1; i < N2; ++i) { 56 | temp1 = coup[i].im + coup[N2-i].im ; 57 | temp2 = coup[N2-i].re - coup[i].re ; 58 | oup[i].re = (coup[i].re + coup[N2-i].re + (temp1 * obj->twiddle2[i].re) + (temp2 * obj->twiddle2[i].im)) / 2.0; 59 | oup[i].im = (coup[i].im - coup[N2-i].im + (temp2 * obj->twiddle2[i].re) - (temp1 * obj->twiddle2[i].im)) / 2.0; 60 | } 61 | 62 | 63 | 64 | oup[N2].re = coup[0].re - coup[0].im; 65 | oup[N2].im = 0.0; 66 | 67 | for (i = 1; i < N2;++i) { 68 | oup[N-i].re = oup[i].re; 69 | oup[N-i].im = -oup[i].im; 70 | } 71 | 72 | 73 | free(cinp); 74 | free(coup); 75 | 76 | } 77 | 78 | void fft_c2r_exec(fft_real_object obj,fft_data *inp,fft_type *oup) { 79 | 80 | fft_data* cinp; 81 | fft_data* coup; 82 | int i,N2,N; 83 | fft_type temp1,temp2; 84 | N2 = obj->cobj->N; 85 | N = N2*2; 86 | 87 | cinp = (fft_data*) malloc (sizeof(fft_data) * N2); 88 | coup = (fft_data*) malloc (sizeof(fft_data) * N2); 89 | 90 | for (i = 0; i < N2; ++i) { 91 | temp1 = -inp[i].im - inp[N2-i].im ; 92 | temp2 = -inp[N2-i].re + inp[i].re ; 93 | cinp[i].re = inp[i].re + inp[N2-i].re + (temp1 * obj->twiddle2[i].re) - (temp2 * obj->twiddle2[i].im); 94 | cinp[i].im = inp[i].im - inp[N2-i].im + (temp2 * obj->twiddle2[i].re) + (temp1 * obj->twiddle2[i].im); 95 | } 96 | 97 | fft_exec(obj->cobj,cinp,coup); 98 | for (i = 0; i < N2; ++i) { 99 | oup[2*i] = coup[i].re; 100 | oup[2*i+1] = coup[i].im; 101 | } 102 | free(cinp); 103 | free(coup); 104 | 105 | 106 | } 107 | 108 | void free_real_fft(fft_real_object object) { 109 | free_fft(object->cobj); 110 | free(object); 111 | } 112 | 113 | -------------------------------------------------------------------------------- /SATnano/src/util/exception.h~: -------------------------------------------------------------------------------- 1 | #ifndef EXCEPTION_H__ 2 | #define EXCEPTION_H__ 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | #include 12 | 13 | #define DO_TRACE_ 14 | #define DO_NOTE_ 15 | #define DO_CLOCK_ 16 | 17 | #ifdef DO_TRACE_ 18 | #define EX_TRACE( MSG,args...) printf(MSG, ##args); fflush(stdout); 19 | #define EX_CUR_WORKSPACE() printf("%s", get_current_dir_name()); fflush(stdout); 20 | #else 21 | #define EX_TRACE( MSG,args...) 22 | #define EX_CUR_WORKSPACE() 23 | #endif 24 | 25 | #ifdef DO_NOTE_ 26 | #define EX_NOTE(X) X 27 | #else 28 | #define EX_NOTE(X) 29 | #endif 30 | 31 | #ifdef DO_CLOCK_ 32 | #define _DASH "------------------------------------------------------------------------------\n" 33 | #define _WAVE "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" 34 | static const char* wday12310[] = {"Sun","Mon","Tue","Wed","Thu"," Fri","Sat"}; 35 | #define EX_TIME_BEGIN( MSG,args...) {time_t time_begin0112;clock_t clock_begin2290;{printf(MSG, ##args); \ 36 | time(&time_begin0112);clock_begin2290 = clock(); struct tm *p; p=localtime(&time_begin0112);\ 37 | printf("[Beginning] %d/%d/%d ", (1900+p->tm_year),(1+p->tm_mon), p->tm_mday); \ 38 | printf("%s %d:%d:%d\n", wday12310[p->tm_wday],p->tm_hour, p->tm_min, p->tm_sec);} fflush(stdout); 39 | #define EX_TIME_END( MSG,args...) time_t time_end8013;clock_t clock_end2520;{printf(MSG, ##args); \ 40 | time(&time_end8013);clock_end2520 = clock(); struct tm *p;p=localtime(&time_end8013); \ 41 | printf("[Finished] %d/%d/%d ", (1900+p->tm_year),(1+p->tm_mon), p->tm_mday); \ 42 | printf("%s %d:%d:%d (time elapse: %ldms)\n", wday12310[p->tm_wday],p->tm_hour, p->tm_min, \ 43 | p->tm_sec, (clock_end2520-clock_begin2290)*1000/CLOCKS_PER_SEC);}} fflush(stdout); 44 | #define EX_BEGIN_CLOCK() clock_t clock_begin2290;{clock_begin2290 = clock();} 45 | #define EX_END_CLOCK() clock_t clock_end2520;{clock_end2520 = clock();} 46 | #define EX_ELAPSE() (clock_end2520-clock_begin2290)*1000/CLOCKS_PER_SEC 47 | #else 48 | #define EX_TIME_BEGIN( MSG,args...) 49 | #define EX_TIME_END( MSG,args...) 50 | #define EX_BEGIN_CLOCK() 51 | #define EX_END_CLOCK() 52 | #define EX_ELAPSE() 0 53 | #endif 54 | 55 | namespace ex{ 56 | 57 | class Exception 58 | { 59 | private: 60 | std::string msg; 61 | public: 62 | Exception(std::string _msg):msg(_msg){} 63 | const char* Msg(){ return msg.c_str();} 64 | }; 65 | 66 | void EX_THROW(const char* x); 67 | 68 | //ex::Puts("", MSG, ##args, "\0"); 69 | // void Puts(const char* msg, ...) 70 | // { 71 | // va_list args; 72 | // char* str; 73 | // va_start(args, msg); 74 | // 75 | // while(1){ 76 | // str = va_arg(args, char*); 77 | // if(strcmp(str, "\0")==0){ 78 | // break; 79 | // } 80 | // std::cout< 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | #include 12 | 13 | #define DO_TRACE_ 14 | #define DO_NOTE_ 15 | #define DO_CLOCK_ 16 | 17 | #define EX_PRINT( MSG,args...) printf(MSG, ##args); fflush(stdout); 18 | #define EX_ERROR( MSG,args...) printf(MSG, ##args); fflush(stderr); 19 | 20 | #ifdef DO_TRACE_ 21 | #define EX_TRACE( MSG,args...) printf(MSG, ##args); fflush(stdout); 22 | #define EX_CUR_WORKSPACE() printf("%s", get_current_dir_name()); fflush(stdout); 23 | #else 24 | #define EX_TRACE( MSG,args...) 25 | #define EX_CUR_WORKSPACE() 26 | #endif 27 | 28 | #ifdef DO_NOTE_ 29 | #define EX_NOTE(X) X 30 | #else 31 | #define EX_NOTE(X) 32 | #endif 33 | 34 | #ifdef DO_CLOCK_ 35 | #define _DASH "------------------------------------------------------------------------------\n" 36 | #define _WAVE "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" 37 | static const char* wday12310[] = {"Sun","Mon","Tue","Wed","Thu"," Fri","Sat"}; 38 | #define EX_TIME_BEGIN( MSG,args...) {time_t time_begin0112;clock_t clock_begin2290;{printf(MSG, ##args); \ 39 | time(&time_begin0112);clock_begin2290 = clock(); struct tm *p; p=localtime(&time_begin0112);\ 40 | printf("[Beginning] %d/%d/%d ", (1900+p->tm_year),(1+p->tm_mon), p->tm_mday); \ 41 | printf("%s %d:%d:%d\n", wday12310[p->tm_wday],p->tm_hour, p->tm_min, p->tm_sec);} fflush(stdout); 42 | #define EX_TIME_END( MSG,args...) time_t time_end8013;clock_t clock_end2520;{printf(MSG, ##args); \ 43 | time(&time_end8013);clock_end2520 = clock(); struct tm *p;p=localtime(&time_end8013); \ 44 | printf("[Finished] %d/%d/%d ", (1900+p->tm_year),(1+p->tm_mon), p->tm_mday); \ 45 | printf("%s %d:%d:%d (time elapse: %ldms)\n", wday12310[p->tm_wday],p->tm_hour, p->tm_min, \ 46 | p->tm_sec, (clock_end2520-clock_begin2290)*1000/CLOCKS_PER_SEC);}} fflush(stdout); 47 | #define EX_BEGIN_CLOCK() clock_t clock_begin2290;{clock_begin2290 = clock();} 48 | #define EX_END_CLOCK() clock_t clock_end2520;{clock_end2520 = clock();} 49 | #define EX_ELAPSE() (clock_end2520-clock_begin2290)*1000/CLOCKS_PER_SEC 50 | #else 51 | #define EX_TIME_BEGIN( MSG,args...) 52 | #define EX_TIME_END( MSG,args...) 53 | #define EX_BEGIN_CLOCK() 54 | #define EX_END_CLOCK() 55 | #define EX_ELAPSE() 0 56 | #endif 57 | 58 | namespace ex{ 59 | 60 | class Exception 61 | { 62 | private: 63 | std::string msg; 64 | public: 65 | Exception(std::string _msg):msg(_msg){} 66 | const char* Msg(){ return msg.c_str();} 67 | }; 68 | 69 | void EX_THROW(const char* x); 70 | 71 | //ex::Puts("", MSG, ##args, "\0"); 72 | // void Puts(const char* msg, ...) 73 | // { 74 | // va_list args; 75 | // char* str; 76 | // va_start(args, msg); 77 | // 78 | // while(1){ 79 | // str = va_arg(args, char*); 80 | // if(strcmp(str, "\0")==0){ 81 | // break; 82 | // } 83 | // std::cout< " 6 | echo "[note1]: snp_sequence could be the same as ref_sequence " 7 | echo "[note2]: in_root shall contain aligned signals in '.reso_new' file " 8 | exit 9 | fi 10 | 11 | 12 | #========= default parameters ===========# 13 | #========= default parameters ===========# 14 | #-> main 15 | SAMPLE_RATE=8 16 | SAMPLE_LEN=50 17 | 18 | #------ read input arguments ---------# 19 | ref_sequence=$1 20 | snp_sequence=$2 21 | in_root=$3 22 | home=`dirname $0` #-> home directory 23 | 24 | #------ mkdir TMP directory ------# 25 | fulnam=`basename $1` 26 | relnam=${fulnam%.*} 27 | txp="${relnam}_PLOT_SIGNAL" 28 | mkdir -p $txp 29 | 30 | 31 | #------ step 0: pre-process ------# 32 | echo "step 0: pre-process" 33 | python $home/util/genome_preprocess.py -i $ref_sequence -o $txp/refseq.fasta -r 1 34 | python $home/util/genome_preprocess.py -i $snp_sequence -o $txp/snpseq.fasta -r 1 35 | ref_len=`tail -n1 $txp/refseq.fasta | wc | awk '{print $3-1}'` 36 | snp_len=`tail -n1 $txp/snpseq.fasta | wc | awk '{print $3-1}'` 37 | if [ $ref_len -ne $snp_len ] 38 | then 39 | echo "ref_len $ref_len not equal to snp_len $snp_len" 40 | exit 1 41 | fi 42 | sample_len=`head -n1 $txp/refseq.fasta | awk '{a=int(a*b);print a}' a=$ref_len b=$SAMPLE_LEN` 43 | 44 | 45 | #------ step 2: transfer ref and snp sequence to signal ------# 46 | echo "step 2: transfer ref and snp sequence to signal" 47 | 48 | #-> 2.1 ref sequence 49 | $home/util/seq2sig -i $txp/refseq.fasta -o $txp/ref.seqsig -k 1 -z 1 -N 1 50 | len=`wc $txp/ref.seqsig | awk '{print $1}'` 51 | rm -f $txp/ref.position 52 | for ((i=1;i<=$len;i++)) 53 | do 54 | echo "$i" >> $txp/ref.position 55 | done 56 | paste -d ' ' $txp/ref.seqsig $txp/ref.position > $txp/ref.seqsig_posi 57 | $home/util/NanoRaw_Label $txp/ref.seqsig_posi 1> $txp/ws1 2> $txp/ws2 58 | $home/util/Signal_Transform $txp/ws2 $txp/ws1 $SAMPLE_LEN $txp/refout 59 | rm -f $txp/ws1 $txp/ws2 60 | #--- snp sequence ---# 61 | $home/util/seq2sig -i $txp/snpseq.fasta -o $txp/snp.seqsig -k 1 -z 1 -N 1 62 | paste -d ' ' $txp/snp.seqsig $txp/ref.position > $txp/snp.seqsig_posi 63 | $home/util/NanoRaw_Label $txp/snp.seqsig_posi 1> $txp/ws1 2> $txp/ws2 64 | $home/util/Signal_Transform $txp/ws2 $txp/ws1 $SAMPLE_LEN $txp/snpout 65 | rm -f $txp/ws1 $txp/ws2 66 | 67 | 68 | #-> 2.3 filter candidate_list to generate final_list 69 | rm -f $txp/reso.signal 70 | ls $in_root/*.reso_new | awk -F"/" '{print $NF}' | cut -d '.' -f 1 > $txp/proc_list 71 | for i in `cat $txp/proc_list` 72 | do 73 | grep -v "#" $in_root/$i.reso_new | awk '{if(NF==6){$1=$1+1; $2=$2+1; print $0}}' > $txp/$i.reso 74 | awk '{print $5" "$0" "$1}' $txp/$i.reso > $txp/$i.reso_posi 75 | $home/util/NanoRaw_Label $txp/$i.reso_posi 1> $txp/ws1 2> $txp/ws2 76 | $home/util/Signal_Transform $txp/ws2 $txp/ws1 $SAMPLE_LEN $txp/tttout 77 | cat $txp/tttout.signal >> 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file_name(argv[1]); 24 | { 25 | fast5::File f; 26 | // 27 | // All fast5 operations are performed inside a try-catch block. This should 28 | // resist various hdf5 errors without leaking memory. 29 | // 30 | try 31 | { 32 | // 33 | // open file in rw mode 34 | // 35 | f.open(file_name, true); 36 | assert(f.is_open()); 37 | assert(f.is_rw()); 38 | // 39 | // find next available basecall group with given prefix 40 | // 41 | string test_bc_grp_prefix = "Test_"; 42 | auto bc_grp_l = f.get_basecall_group_list(); 43 | set< string > test_bc_grp_suffix_s; 44 | for (const auto& bc_grp : bc_grp_l) 45 | { 46 | if (bc_grp.compare(0, test_bc_grp_prefix.size(), test_bc_grp_prefix) == 0) 47 | { 48 | cerr << "found group: " << test_bc_grp_prefix + bc_grp.substr(test_bc_grp_prefix.size()) << endl; 49 | } 50 | test_bc_grp_suffix_s.insert(bc_grp.substr(test_bc_grp_prefix.size())); 51 | } 52 | string test_bc_grp_suffix; 53 | for (unsigned i = 0; i < 1000; ++i) 54 | { 55 | ostringstream os; 56 | os << setw(3) << setfill('0') << i; 57 | if (test_bc_grp_suffix_s.count(os.str()) == 0) 58 | { 59 | test_bc_grp_suffix = os.str(); 60 | break; 61 | } 62 | } 63 | assert(not test_bc_grp_suffix.empty()); 64 | clog << "using group: " << test_bc_grp_prefix + test_bc_grp_suffix << endl; 65 | // 66 | // add basecall seq 67 | // 68 | f.add_basecall_seq(0, test_bc_grp_prefix + test_bc_grp_suffix, "test_name", "ACGT"); 69 | // 70 | // add basecall events 71 | // 72 | vector< fast5::Basecall_Event > ev(3, {55.0, 1.0, 0.05, 0.01, .5, 0, array< char, 8 >{"ACGTA"}}); 73 | f.add_basecall_events(0, test_bc_grp_prefix + test_bc_grp_suffix, ev); 74 | // 75 | // add basecall pore model 76 | // 77 | vector< fast5::Basecall_Model_State > mod(3, {56.0, 1.0, 42.0, 1.0, array< char, 8 >{"ACGTA"}}); 78 | f.add_basecall_model(0, test_bc_grp_prefix + test_bc_grp_suffix, mod); 79 | // 80 | // add basecall pore model params 81 | // 82 | fast5::Basecall_Model_Params params{1.0, 0.0, 0.0, 1.0, .9, .9}; 83 | f.add_basecall_model_params(0, test_bc_grp_prefix + test_bc_grp_suffix, params); 84 | // 85 | // add basecall model file 86 | // 87 | f.add_basecall_model_file(0, test_bc_grp_prefix + test_bc_grp_suffix, "/dev/null"); 88 | } 89 | catch (hdf5_tools::Exception& e) 90 | { 91 | cout << "hdf5 error: " << e.what() << endl; 92 | } 93 | // 94 | // fast5 file is closed by its destructor at the end of this scope 95 | // 96 | } 97 | assert(hdf5_tools::File::get_object_count() == 0); 98 | } 99 | -------------------------------------------------------------------------------- /SATnano/build/lib/wavelib/src/CMakeFiles/wavelib.dir/C.includecache: -------------------------------------------------------------------------------- 1 | #IncludeRegexLine: ^[ ]*#[ ]*(include|import)[ ]*[<"]([^">]+)([">]) 2 | 3 | #IncludeRegexScan: ^.*$ 4 | 5 | #IncludeRegexComplain: ^$ 6 | 7 | #IncludeRegexTransform: 8 | 9 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/conv.c 10 | conv.h 11 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/conv.h 12 | 13 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/conv.h 14 | real.h 15 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/real.h 16 | 17 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/cwt.c 18 | cwt.h 19 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/cwt.h 20 | 21 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/cwt.h 22 | wavefunc.h 23 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavefunc.h 24 | 25 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/cwtmath.c 26 | cwtmath.h 27 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/cwtmath.h 28 | 29 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/cwtmath.h 30 | wtmath.h 31 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wtmath.h 32 | hsfft.h 33 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/hsfft.h 34 | 35 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/hsfft.c 36 | hsfft.h 37 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/hsfft.h 38 | 39 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/hsfft.h 40 | stdlib.h 41 | - 42 | math.h 43 | - 44 | string.h 45 | - 46 | 47 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/real.c 48 | stdio.h 49 | - 50 | real.h 51 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/real.h 52 | 53 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/real.h 54 | hsfft.h 55 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/hsfft.h 56 | 57 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavefilt.c 58 | wavefilt.h 59 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavefilt.h 60 | 61 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavefilt.h 62 | stdio.h 63 | - 64 | conv.h 65 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/conv.h 66 | math.h 67 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/math.h 68 | 69 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavefunc.c 70 | wavefunc.h 71 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavefunc.h 72 | 73 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavefunc.h 74 | cwtmath.h 75 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/cwtmath.h 76 | 77 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavelib.c 78 | wavelib.h 79 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavelib.h 80 | 81 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavelib.h 82 | wtmath.h 83 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wtmath.h 84 | cwt.h 85 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/cwt.h 86 | 87 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wtmath.c 88 | wtmath.h 89 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wtmath.h 90 | 91 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wtmath.h 92 | wavefilt.h 93 | /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/lib/wavelib/src/wavefilt.h 94 | 95 | -------------------------------------------------------------------------------- /SATnano/lib/wavelib/src/conv.c: -------------------------------------------------------------------------------- 1 | /* 2 | * conv.c 3 | * 4 | * Created on: May 1, 2013 5 | * Author: Rafat Hussain 6 | */ 7 | 8 | #include "conv.h" 9 | 10 | int factorf(int M) { 11 | int N; 12 | N = M; 13 | while (N%7 == 0){ 14 | N = N/7; 15 | } 16 | while (N%3 == 0){ 17 | N = N/3; 18 | } 19 | while (N%5 == 0){ 20 | N = N/5; 21 | } 22 | while (N%2 == 0){ 23 | N = N/2; 24 | } 25 | 26 | return N; 27 | } 28 | 29 | 30 | int findnext(int M) { 31 | int N; 32 | N = M; 33 | 34 | while (factorf(N) != 1) { 35 | ++N; 36 | } 37 | 38 | return N; 39 | 40 | } 41 | 42 | int findnexte(int M) { 43 | int N; 44 | N = M; 45 | 46 | while (factorf(N) != 1 || N%2 != 0) { 47 | ++N; 48 | } 49 | 50 | return N; 51 | 52 | } 53 | 54 | 55 | conv_object conv_init(int N, int L) { 56 | 57 | conv_object obj = NULL; 58 | int conv_len; 59 | conv_len = N + L - 1; 60 | 61 | obj = (conv_object) malloc (sizeof(struct conv_set)); 62 | 63 | //obj->clen = npow2(conv_len); 64 | //obj->clen = conv_len; 65 | obj->clen = findnexte(conv_len); 66 | obj->ilen1 = N; 67 | obj->ilen2 = L; 68 | 69 | obj->fobj = fft_real_init(obj->clen,1); 70 | obj->iobj = fft_real_init(obj->clen,-1); 71 | 72 | return obj; 73 | 74 | } 75 | 76 | void conv_directx(fft_type *inp1,int N, fft_type *inp2, int L,fft_type *oup){ 77 | int M,k,n; 78 | 79 | M = N + L - 1; 80 | 81 | for (k = 0; k < M;++k) { 82 | oup[k] = 0.0; 83 | for ( n = 0; n < N; ++n) { 84 | if ( (k-n) >= 0 && (k-n) < L ) { 85 | oup[k]+= inp1[n] * inp2[k-n]; 86 | } 87 | } 88 | 89 | } 90 | 91 | } 92 | 93 | void conv_direct(fft_type *inp1,int N, fft_type *inp2, int L,fft_type *oup) { 94 | 95 | int M,k,m,i; 96 | fft_type t1,tmin; 97 | 98 | M = N + L -1; 99 | i = 0; 100 | 101 | if (N >= L) { 102 | 103 | for (k = 0; k < L; k++) { 104 | oup[k] = 0.0; 105 | for (m = 0; m <= k;m++) { 106 | oup[k]+= inp1[m] * inp2[k-m]; 107 | } 108 | } 109 | 110 | for (k = L; k < M; k++) { 111 | oup[k] = 0.0; 112 | i++; 113 | t1 = L + i; 114 | tmin = MIN(t1,N); 115 | for (m = i; m < tmin;m++) { 116 | oup[k]+= inp1[m] * inp2[k-m]; 117 | } 118 | } 119 | 120 | 121 | } else { 122 | for (k = 0; k < N; k++) { 123 | oup[k] = 0.0; 124 | for (m = 0; m <= k;m++) { 125 | oup[k]+= inp2[m] * inp1[k-m]; 126 | } 127 | } 128 | 129 | for (k = N; k < M; k++) { 130 | oup[k] = 0.0; 131 | i++; 132 | t1 = N + i; 133 | tmin = MIN(t1,L); 134 | for (m = i; m < tmin;m++) { 135 | oup[k]+= inp2[m] * inp1[k-m]; 136 | } 137 | } 138 | 139 | } 140 | 141 | 142 | } 143 | 144 | 145 | void conv_fft(const conv_object obj,fft_type *inp1,fft_type *inp2,fft_type *oup) { 146 | int i,N,L1,L2,ls; 147 | fft_type* a; 148 | fft_type* b; 149 | fft_data* c; 150 | fft_data* ao; 151 | fft_data* bo; 152 | fft_type* co; 153 | 154 | N = obj->clen; 155 | L1 = obj->ilen1; 156 | L2 = obj->ilen2; 157 | ls = L1 + L2 - 1; 158 | 159 | a = (fft_type*) malloc (sizeof(fft_data) * N); 160 | b = (fft_type*) malloc (sizeof(fft_data) * N); 161 | c = (fft_data*) malloc (sizeof(fft_data) * N); 162 | ao = (fft_data*) malloc (sizeof(fft_data) * N); 163 | bo = (fft_data*) malloc (sizeof(fft_data) * N); 164 | co = (fft_type*) malloc (sizeof(fft_data) * N); 165 | 166 | for (i = 0; i < N;i++) { 167 | if (i < L1) { 168 | a[i] = inp1[i]; 169 | } else { 170 | a[i] = 0.0; 171 | } 172 | 173 | if (i < L2) { 174 | b[i] = inp2[i]; 175 | } else { 176 | b[i] = 0.0; 177 | } 178 | 179 | } 180 | 181 | fft_r2c_exec(obj->fobj,a,ao); 182 | fft_r2c_exec(obj->fobj,b,bo); 183 | 184 | for (i = 0; i < N;i++) { 185 | c[i].re = ao[i].re * bo[i].re - ao[i].im * bo[i].im; 186 | c[i].im = ao[i].im * bo[i].re + ao[i].re * bo[i].im; 187 | } 188 | 189 | fft_c2r_exec(obj->iobj,c,co); 190 | 191 | for (i = 0; i < ls;i++) { 192 | oup[i] = co[i]/N; 193 | } 194 | 195 | free(a); 196 | free(b); 197 | free(c); 198 | free(ao); 199 | free(bo); 200 | free(co); 201 | 202 | 203 | } 204 | 205 | 206 | void free_conv(conv_object object) { 207 | free_real_fft(object->fobj); 208 | free_real_fft(object->iobj); 209 | free(object); 210 | } 211 | -------------------------------------------------------------------------------- /plot_nanofigure/util/PlotSignal_SNP.py: -------------------------------------------------------------------------------- 1 | import os 2 | import sys 3 | import numpy as np 4 | import matplotlib 5 | matplotlib.use('Agg') 6 | import matplotlib.pyplot as plt 7 | 8 | 9 | #----- function int2kmer --------# 10 | def int2kmer(input_num,mer_k = 5): 11 | kmer = '' 12 | kmer_dict = ['A','C','G','T'] 13 | for i in range(mer_k): 14 | kmer = kmer_dict[input_num%4]+kmer 15 | input_num = input_num/4 16 | return kmer 17 | 18 | 19 | 20 | #=========== example ===========# 21 | """ 22 | 417 406 403 407 426 501 497 508 492 493 23 | """ 24 | 25 | #----- load signal data ----# 26 | def load_signal(infile): 27 | #-> read infile 28 | fh = open(infile) 29 | nanoraw_signal = [] 30 | for line in list(fh): 31 | signal = line.split(' ') 32 | nanoraw_signal.append(signal) 33 | #-> return 34 | return nanoraw_signal 35 | 36 | 37 | #=========== example ===========# 38 | """ 39 | 1 2 C 40 | 2 6 C 41 | 6 55 C 42 | 55 64 T 43 | 64 68 G 44 | 68 69 G 45 | """ 46 | 47 | #----- load range data ----# 48 | def load_range(infile, base = 0): 49 | #-> read infile 50 | fh = open(infile) 51 | input_beg = list() 52 | input_end = list() 53 | input_lab = list() 54 | for line in fh: 55 | split_line = line.split() 56 | input_beg.append(int(split_line[0])+base) 57 | input_end.append(int(split_line[1])+base) 58 | input_lab.append(split_line[2]) 59 | #-> return 60 | return input_beg,input_end,input_lab 61 | 62 | 63 | 64 | #============= plot the figure =============# 65 | def plot_figure(signal, beg,end,lab, output, start=None, termi=None): 66 | size=2000 67 | part=50 68 | color_dict = {'A':'red','C':'yellow','G':'green','T':'blue'} 69 | orilen=len(signal[0]) 70 | #-> determine start and end if None 71 | if start is None: 72 | start=0 73 | if termi is None: 74 | termi=orilen-1 75 | if start < 0: 76 | start=0 77 | if termi >= orilen: 78 | termi=orilen-1 79 | #-> get subsequence of the input signal 80 | length=termi-start+1 81 | if length%size == 0: 82 | col=length/size 83 | else: 84 | col=int(length/size)+1 85 | #-> set the x-axis 86 | scalar=np.array([0, 5, 10, 15, 20, 25, 30, 35, 40]) 87 | srange=scalar*50 88 | 89 | #-> plot the figure 90 | f,axs = plt.subplots(col,1,sharex = False,figsize=(20, 4*col), squeeze=False) 91 | for i in range(col): 92 | #--| get cur_start and cur_end 93 | cur_start=start+i*size 94 | cur_end=min(cur_start+size,termi) 95 | #--| plot cursignal 96 | cur=0 97 | for k in signal: 98 | cursignal=np.zeros(size) 99 | cursignal[0:cur_end-cur_start]=k[cur_start:cur_end] 100 | #---- plot 1st and 2nd signal with bold color ----# 101 | if cur == 0: 102 | axs[i,0].plot(cursignal, linewidth=5.0, color='red') 103 | elif cur == 1: 104 | axs[i,0].plot(cursignal, linewidth=2.5, color='green') 105 | else: 106 | axs[i,0].plot(cursignal, linewidth=0.2, color='black') 107 | cur=cur+1 108 | axs[i,0].set_ylim([-3,3]) 109 | #--| plot curlabel 110 | for idx,val in enumerate(beg): 111 | if val>=cur_start and val save the figure 120 | f.savefig(output) 121 | 122 | 123 | 124 | #------- usage -------# 125 | def Usage(): 126 | print 'python PlotSignal.py ' 127 | print 'signal_label : the file contains signal and label ' 128 | print 'start_end_char : the file contains start, end, and char ' 129 | print 'output.png : output PNG file' 130 | 131 | 132 | #------- main --------# 133 | def main(argv): 134 | if len(argv) != 5: 135 | Usage() 136 | sys.exit(-1) 137 | #-> get input arguments 138 | signal_label=argv[0] 139 | start_end_char=argv[1] 140 | output=argv[2] 141 | start=int(argv[3]) 142 | termi=int(argv[4]) 143 | #-> load input files 144 | nanoraw_signal=load_signal(signal_label) 145 | input_beg,input_end,input_lab=load_range(start_end_char) 146 | #-> process 147 | plot_figure(nanoraw_signal,input_beg,input_end,input_lab,output,start,termi) 148 | 149 | 150 | #-------------- python main ---------------# 151 | if __name__ == "__main__": 152 | ## read and , plot the figure 153 | main(sys.argv[1:]) 154 | 155 | 156 | 157 | -------------------------------------------------------------------------------- /SATnano/build/lib/wavelib/src/CMakeFiles/wavelib.dir/depend.make: -------------------------------------------------------------------------------- 1 | # CMAKE generated file: DO NOT EDIT! 2 | # Generated by "Unix Makefiles" Generator, CMake Version 2.6 3 | 4 | lib/wavelib/src/CMakeFiles/wavelib.dir/conv.c.o: ../lib/wavelib/src/conv.c 5 | lib/wavelib/src/CMakeFiles/wavelib.dir/conv.c.o: ../lib/wavelib/src/conv.h 6 | lib/wavelib/src/CMakeFiles/wavelib.dir/conv.c.o: ../lib/wavelib/src/hsfft.h 7 | lib/wavelib/src/CMakeFiles/wavelib.dir/conv.c.o: ../lib/wavelib/src/real.h 8 | 9 | lib/wavelib/src/CMakeFiles/wavelib.dir/cwt.c.o: ../lib/wavelib/src/conv.h 10 | 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../lib/wavelib/src/wavefilt.h 64 | lib/wavelib/src/CMakeFiles/wavelib.dir/wtmath.c.o: ../lib/wavelib/src/wtmath.c 65 | lib/wavelib/src/CMakeFiles/wavelib.dir/wtmath.c.o: ../lib/wavelib/src/wtmath.h 66 | 67 | -------------------------------------------------------------------------------- /plot_nanofigure/source_code/NanoRaw_Label.cpp: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | using namespace std; 12 | 13 | 14 | //-------- utility ------// 15 | void getBaseName(string &in,string &out,char slash,char dot) 16 | { 17 | int i,j; 18 | int len=(int)in.length(); 19 | for(i=len-1;i>=0;i--) 20 | { 21 | if(in[i]==slash)break; 22 | } 23 | i++; 24 | for(j=len-1;j>=0;j--) 25 | { 26 | if(in[j]==dot)break; 27 | } 28 | if(j==-1)j=len; 29 | out=in.substr(i,j-i); 30 | } 31 | void getRootName(string &in,string &out,char slash) 32 | { 33 | int i; 34 | int len=(int)in.length(); 35 | for(i=len-1;i>=0;i--) 36 | { 37 | if(in[i]==slash)break; 38 | } 39 | if(i<=0)out="."; 40 | else out=in.substr(0,i); 41 | } 42 | 43 | int Parse_Str(string &in,vector &out) 44 | { 45 | istringstream www(in); 46 | out.clear(); 47 | int count=0; 48 | for(;;) 49 | { 50 | string buf; 51 | if(! (www>>buf) )break; 52 | out.push_back(buf); 53 | count++; 54 | } 55 | return count; 56 | } 57 | 58 | //----- Z-score ----// 59 | void Z_score(vector &in,double &mean,double &vari) 60 | { 61 | //init 62 | mean=0; 63 | vari=1; 64 | //proc 65 | int i; 66 | int size=(int)in.size(); 67 | if(size==0)return; 68 | //-> calculate mean 69 | for(i=0;i calculate vari 72 | vari=0; 73 | for(i=0;i calculate Z-score 76 | for(i=0;i input 83 | /* 84 | 385 288 | 91 9 | -0.915353 -1.17514 diff: 0.25979 CAGAA 9 85 | 303 131 | 92 10 | -2.08046 -1.82747 diff: 0.25299 AGAAT 10 86 | 285 527 | 93 11 | -2.33622 -1.86196 diff: 0.474257 GAATT 11 87 | 278 527 | 94 11 | -2.43568 -1.86196 diff: 0.573718 GAATT 11 88 | 294 527 | 95 11 | -2.20834 -1.86196 diff: 0.34638 GAATT 11 89 | 369 527 | 96 11 | -1.14269 -1.86196 diff: 0.719268 GAATT 11 90 | 433 63 | 97 12 | -0.233338 0.427542 diff: 0.66088 AATTT 12 91 | 399 63 | 98 12 | -0.716432 0.427542 diff: 1.14397 AATTT 12 92 | 481 63 | 99 12 | 0.448676 0.427542 diff: 0.0211343 AATTT 12 93 | .... 94 | */ 95 | //-> output 96 | /* 97 | 107 111 C 98 | 111 123 G 99 | 123 131 C 100 | 131 160 C 101 | .... 102 | */ 103 | 104 | void NanoRaw_Label(string &in) 105 | { 106 | //read 107 | ifstream fin; 108 | string buf,temp; 109 | fin.open(in.c_str(), ios::in); 110 | if(fin.fail()!=0) 111 | { 112 | fprintf(stderr,"list %s not found!!\n",in.c_str()); 113 | exit(-1); 114 | } 115 | //read 116 | int first=1; 117 | string prev=""; 118 | string curr=""; 119 | string prev_rec=""; 120 | int start=0; 121 | int count=0; 122 | vector signal; 123 | for(;;) 124 | { 125 | if(!getline(fin,buf,'\n'))break; 126 | istringstream www(buf); 127 | vector out; 128 | int retv=Parse_Str(buf,out); 129 | curr=out[retv-1]; 130 | if(first==1) 131 | { 132 | prev=curr; 133 | prev_rec=out[retv-2]; 134 | first=0; 135 | } 136 | else 137 | { 138 | if(prev!=curr) //-> output 139 | { 140 | printf("%d %d %c\n",start+1,count+1,prev_rec[2]); 141 | start=count; 142 | prev=curr; 143 | prev_rec=out[retv-2]; 144 | } 145 | } 146 | //fprintf(stderr,"%s\n",out[0].c_str()); 147 | signal.push_back(atof(out[0].c_str())); 148 | count++; 149 | } 150 | //termi 151 | if(prev_rec!="") //-> output 152 | { 153 | printf("%d %d %c\n",start+1,count+1,prev_rec[2]); 154 | } 155 | //--- transfer to Z-score ---// 156 | double mean,vari; 157 | Z_score(signal,mean,vari); 158 | for(int i=0;i<(int)signal.size();i++)fprintf(stderr,"%lf\n",signal[i]); 159 | } 160 | 161 | 162 | //---------- main ----------// 163 | int main(int argc,char **argv) 164 | { 165 | //---- NanoRaw_Label ----// 166 | { 167 | if(argc<2) 168 | { 169 | fprintf(stderr,"NanoRaw_Label \n"); 170 | exit(-1); 171 | } 172 | string infile=argv[1]; 173 | //proc 174 | NanoRaw_Label(infile); 175 | //exit 176 | exit(0); 177 | } 178 | } 179 | 180 | -------------------------------------------------------------------------------- /SATnano/src/proc/proc.h: -------------------------------------------------------------------------------- 1 | #ifndef PROC_H__ 2 | #define PROC_H__ 3 | 4 | #include "io.h" 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | // #include 11 | #include "wavelib.h" 12 | 13 | namespace g{ 14 | namespace proc{ 15 | // void SpectrumAmplitude(std::vector& signals, std::vector& amplitude); 16 | // 17 | // void SpectrumAmplitude(double* signals, int size, std::vector& amplitude); 18 | 19 | void ZScoreNormalize(std::vector& signals, double* avg = NULL, double* stdev = NULL); 20 | 21 | void Resample(int upfactor, int downfactor, const std::vector& input, std::vector& output); 22 | 23 | void ScaleSignalAmplitude(std::vector& signals, double scale = 1); 24 | 25 | void MedianFilter(std::vector& signals, int width = 5); 26 | 27 | void WaveDenoise(std::vector& signals, bool soft = true); 28 | 29 | void RemoveHotSpot(std::vector& signals, int thre = 5); 30 | 31 | void LaplaceDiff(const std::vector& raw, std::vector& ldiff); 32 | 33 | void Diff(const std::vector& raw, std::vector& diff); 34 | 35 | double L2Distance(const std::vector& sig1, const std::vector& sig2); 36 | double L1Distance(const std::vector& sig1, const std::vector& sig2); 37 | 38 | void PeakPick(const std::vector& raw, std::vector >& peaks); 39 | 40 | void LocalMaximum(const std::vector& raw, std::vector >& peaks); 41 | 42 | /** @scale0: level0 pyramind scale; @dscale: scale_i = scale0*(2^{i*dsacle} ); @npyr: total number of pyramind*/ 43 | void CWTAnalysis(const std::vector& raw, std::vector >& output, double scale0, double dscale = 1, int npyr = 1); 44 | 45 | /** @scale0: level0 pyramind scale; @dscale: scale_i = scale0*(2^{i*dsacle} ); @npyr: total number of pyramind*/ 46 | void CWTAnalysisEsp(const std::vector& raw, std::vector >& output, double scale0, double dscale = 1, int npyr = 1); 47 | 48 | void DumpCWTSpectrogram(const std::vector >& waves, char* filename); 49 | 50 | double DynamicTimeWarping(const std::vector& seq1, const std::vector& seq2, std::vector >& alignment); 51 | 52 | double DynamicTimeWarpingR(const std::vector& seq1, const std::vector& seq2, std::vector >& alignment); 53 | 54 | double SubsequenceDynamicTimeWarping(const std::vector& seq1, const std::vector& seq2, 55 | std::vector& local_score, std::vector >* alignment = NULL); 56 | 57 | void SquareBoundGeneration(std::vector >& cosali, int radius, std::vector >& bound); 58 | 59 | void BoundGeneration(std::vector >& cosali, int radius, std::vector >& bound); 60 | 61 | double BoundDynamicTimeWarping(const std::vector& seq1, const std::vector& seq2, const std::vector >& bound, std::vector >& alignment); 62 | 63 | /** Left path is blocked*/ 64 | double BoundDynamicTimeWarpingR(const std::vector& seq1, const std::vector& seq2, const std::vector >& bound, std::vector >& alignment); 65 | 66 | double CWDynamicTimeWarping(const std::vector& seq1, const std::vector& seq2, std::vector >& alignment, 67 | double scale0 = 1.414, double l = 3, double radius = 50, int boundmode = 1, bool left_constrained = false); 68 | 69 | double FastInquiry(const std::vector& reference, const std::vector& peer, std::vector >& alignment, double scale_diff = 8, 70 | int seed_num = 3, int seed_length = 128, double radius = 50, int boundmode = 1, bool left_constrained = false); 71 | 72 | double DirectInquiry(const std::vector& reference, const std::vector& peer, std::vector >& alignment, double scale_diff = 8, 73 | double radius = 50, int boundmode = 1, bool left_constrained = false); 74 | 75 | // double NaiveInquiry(const std::vector& reference, const std::vector& peer, std::vector >& indexes, int k_th = 3, double ratio = 8, 76 | // double scale0 = 1.414, double l = 3, double radius = 50, int boundmode = 1, bool left_constrained = false); 77 | 78 | /*alignment pair order: >& alignment, const std::vector >& ground_truth, double range = 0.85); 80 | 81 | void DumpTimeSeries(const std::vector& signal, const char* path); 82 | } 83 | 84 | } 85 | 86 | 87 | #endif 88 | -------------------------------------------------------------------------------- /SATnano/src/fastalign/main.cpp: -------------------------------------------------------------------------------- 1 | #include "opts.h" 2 | #include 3 | #include 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include "proc/proc.h" 9 | #include "util/exception.h" 10 | #include "6mer/6mer_index.h" 11 | #include "wavelib.h" 12 | #include 13 | #include 14 | #include 15 | #include 16 | 17 | using namespace std; 18 | 19 | void WriteSequenceAlignment(const char* output, const vector& genomes, const std::vector& reference_orig, const std::vector& peer_orig, 20 | const std::vector& reference, const std::vector& peer, vector >& alignment) 21 | { 22 | std::ofstream o(output); 23 | 24 | double diff, avgdiff = 0; 25 | 26 | for(int i = 0; i < alignment.size() && alignment[i].first+6 < genomes.size(); i++){ 27 | o<& genomes, const std::vector& reference_orig, 39 | const std::vector& peer_orig, vector >& alignment) 40 | { 41 | std::ofstream o(output); 42 | 43 | o< genomes; 70 | std::vector reference; //reference: genome 71 | 72 | EX_TIME_BEGIN("\nTransform genomes to signal sequence..."); 73 | 74 | if(strcmp(g::io::GetFileExtension(opts.input).c_str(), "fast5") == 0 75 | && g::io::ReadFast5ATCG(opts.input, genomes)){ 76 | EX_TRACE("%ld genomes are readed.\n", genomes.size()); 77 | } 78 | else if(g::io::ReadATCG(opts.input, genomes)){ 79 | EX_TRACE("%ld genomes are readed.\n", genomes.size()); 80 | } 81 | else{ 82 | EX_TRACE("Cannot open %s.\n", opts.input); 83 | return -1; 84 | } 85 | 86 | g::io::Genomes2SignalSequence(genomes, reference, 1); 87 | g::io::WriteSignalSequence("genome2sig.result", reference); 88 | 89 | EX_TIME_END("Transform genomes to signal sequence..."); 90 | EX_TIME_BEGIN("Continous Wavelet Dynamic Time Warping...") 91 | 92 | std::vector peer; //peer: nanopore signal 93 | 94 | if(strcmp(g::io::GetFileExtension(opts.peer).c_str(), "fast5") == 0 95 | && !g::io::ReadFast5SignalSequence(opts.peer, peer)){ 96 | EX_TRACE("Cannot open %s.\n", opts.peer); 97 | return -1; 98 | } 99 | else if(!g::io::ReadSignalSequence(opts.peer, peer)){ 100 | EX_TRACE("Cannot open %s.\n", opts.peer); 101 | return -1; 102 | } 103 | else{ 104 | EX_TRACE("%ld signals are readed.\n", peer.size()); 105 | } 106 | 107 | std::vector reference_orig(reference), peer_orig(peer); 108 | 109 | g::proc::ZScoreNormalize(reference); 110 | g::proc::ZScoreNormalize(peer); 111 | 112 | std::vector > alignment; 113 | double ndist = g::proc::CWDynamicTimeWarping(reference, peer, alignment, opts.scale0, opts.level, opts.radius, 1, true); //true); 114 | 115 | // WriteSequenceAlignment(opts.output, genomes, reference_orig, peer_orig, reference, peer, alignment); 116 | 117 | if(!opts.fundamental){ 118 | WriteSequenceAlignment(opts.output, genomes, reference_orig, peer_orig, reference, peer, alignment); 119 | } 120 | else{ 121 | WriteFundamentalAlignment(opts.output, ndist, genomes, reference_orig, peer_orig, alignment); 122 | } 123 | 124 | EX_TIME_END("Continous Wavelet Dynamic Time Warping...") 125 | 126 | return 0; 127 | } 128 | 129 | -------------------------------------------------------------------------------- /SATnano/src/fastalign/opts.h: -------------------------------------------------------------------------------- 1 | #ifndef OPTS_H__ 2 | #define OPTS_H__ 3 | 4 | #include 5 | #include 6 | #include 7 | extern "C" { 8 | #include 9 | } 10 | #include "util/exception.h" 11 | 12 | struct options { 13 | char input[255]; 14 | char peer[255]; 15 | char output[255]; 16 | int radius; 17 | int level; 18 | float scale0; 19 | int fundamental; 20 | }; 21 | 22 | inline int GetOpts(int argc, char **argv, options* opts_) { 23 | 24 | static struct option longopts[] = { 25 | { "help", no_argument, NULL, 'h' }, 26 | { "input", required_argument, NULL, 'i' }, 27 | { "peer", required_argument, NULL, 'p' }, 28 | { "output", required_argument, NULL, 'o' }, 29 | { "radius", required_argument, NULL, 'r' }, 30 | { "level", required_argument, NULL, 'l' }, 31 | { "scale", required_argument, NULL, 's' }, 32 | { "fundamental", no_argument, NULL, 'f' }, 33 | { NULL, 0, NULL, 0 } 34 | }; 35 | 36 | if((argc != 7 && argc != 8 && argc != 9 && argc != 10 && argc != 11 && argc != 12 && argc != 13 && argc != 14) 37 | && argc >= 3 || (argc == 2 && argv[1][0] != '-' && argv[1][1] != 'h') || argc == 1) { 38 | EX_TRACE("[-i INPUT (GENOME) SEQUENCE][-p PEER SIGNAL][-o OUTPUT]([-r NEIGHBOUR RADIUS])([-l LEVEL])(-s SCALE)([-f FUNDAMENTAL OUTPUT])\n"); 39 | return -1; 40 | } 41 | 42 | int ch; 43 | while((ch = getopt_long(argc, argv, "hi:p:o:r:l:s:f", longopts, NULL))!= -1) { 44 | switch(ch) { 45 | 46 | case '?': 47 | EX_TRACE("Invalid option '%s'.", argv[optind-1]); 48 | return -1; 49 | 50 | case ':': 51 | EX_TRACE("Missing option argument for '%s'.", argv[optind-1]); 52 | return -1; 53 | 54 | case 'h': 55 | EX_TRACE("[-i INPUT (GENOME) SEQUENCE][-p PEER SIGNAL][-o OUTPUT]([-r NEIGHBOUR RADIUS])([-l LEVEL])(-s SCALE)([-f FUNDAMENTAL OUTPUT])\n" 56 | "INPUT (GENOME) SEQUENCE: reference sequence i.e. ATCG...;\n" 57 | "PEER SIGNAL: (nanopore) signal that will be transformed to align with reference;\n" 58 | "OUTPUT: signal alignment result;\n" 59 | "NEIGHBOUR RADIUS: warp search radius (default 15);\n" 60 | "LEVEL: sampling level in continous wavelet (default 3);\n" 61 | "SCALE: base scale in continous wavelet (default 1.1415);\n" 62 | "FUNDAMENTAL OUTPUT: set the output in the format for non-standard signal detection (no param).\n" 63 | "\n#WARNING!!! SAT now accepts fast5 files as input: \n" 64 | " for \"-i xxx.fast5\", the ATCG sequence will only be read;\n" 65 | " for \"-p xxx.fast5\", the raw signal will only be read.\n" 66 | ); 67 | 68 | return 0; 69 | 70 | case 'i': 71 | { 72 | std::istringstream iss(optarg); 73 | iss >> opts_->input; 74 | if(iss.fail()) 75 | EX_TRACE("Invalid argument '%s'.", optarg); 76 | } 77 | break; 78 | 79 | case 'p': 80 | { 81 | std::istringstream iss(optarg); 82 | iss >> opts_->peer; 83 | if(iss.fail()) 84 | EX_TRACE("Invalid argument '%s'.", optarg); 85 | } 86 | break; 87 | 88 | case 'o': 89 | { 90 | std::istringstream iss(optarg); 91 | iss >> opts_->output; 92 | if(iss.fail()) 93 | EX_TRACE("Invalid argument '%s'.", optarg); 94 | } 95 | break; 96 | 97 | case 'r': 98 | { 99 | std::istringstream iss(optarg); 100 | iss >> opts_->radius; 101 | if(iss.fail()) 102 | EX_TRACE("Invalid argument '%s'.", optarg); 103 | } 104 | break; 105 | 106 | case 'l': 107 | { 108 | std::istringstream iss(optarg); 109 | iss >> opts_->level; 110 | if(iss.fail()) 111 | EX_TRACE("Invalid argument '%s'.", optarg); 112 | } 113 | break; 114 | 115 | case 's': 116 | { 117 | std::istringstream iss(optarg); 118 | iss >> opts_->scale0; 119 | if(iss.fail()) 120 | EX_TRACE("Invalid argument '%s'.", optarg); 121 | } 122 | break; 123 | 124 | case 'f': 125 | { 126 | opts_->fundamental = 1; 127 | } 128 | break; 129 | 130 | case 0: 131 | break; 132 | 133 | default: 134 | assert(false); 135 | } 136 | } 137 | return 1; 138 | } 139 | 140 | #endif -------------------------------------------------------------------------------- /SATnano/lib/fast5/include/fast5/Bit_Packer.hpp: -------------------------------------------------------------------------------- 1 | // 2 | // Part of: https://github.com/mateidavid/fast5 3 | // 4 | // Copyright (c) 2015-2017 Matei David, Ontario Institute for Cancer Research 5 | // MIT License 6 | // 7 | 8 | #ifndef __BIT_PACKER_HPP 9 | #define __BIT_PACKER_HPP 10 | 11 | #include 12 | #include 13 | #include 14 | #include 15 | #include 16 | #include 17 | #include 18 | #include 19 | 20 | #include "logger.hpp" 21 | 22 | namespace fast5 23 | { 24 | 25 | class Bit_Packer 26 | { 27 | public: 28 | typedef std::vector< std::uint8_t > Code_Type; 29 | typedef std::map< std::string, std::string > Code_Params_Type; 30 | 31 | template < typename Int_Type > 32 | std::pair< Code_Type, Code_Params_Type > 33 | encode(std::vector< Int_Type > const & v, unsigned num_bits) const 34 | { 35 | Code_Type res; 36 | Code_Params_Type res_params; 37 | res_params["packer"] = "bit_packer"; 38 | num_bits = std::min(num_bits, (unsigned)sizeof(Int_Type) * 8); 39 | std::ostringstream oss; 40 | oss << num_bits; 41 | res_params["num_bits"] = oss.str(); 42 | oss.str(""); 43 | oss << v.size(); 44 | res_params["size"] = oss.str(); 45 | long long unsigned buff = 0; 46 | unsigned buff_len = 0; 47 | auto val_mask = (1llu << num_bits) - 1; 48 | for (unsigned i = 0; i < v.size(); ++i) 49 | { 50 | // flush out buff 51 | while (buff_len >= 8) 52 | { 53 | res.push_back(buff & 0xFF); 54 | buff >>= 8; 55 | buff_len -= 8; 56 | } 57 | assert(buff_len < 8); 58 | long long unsigned x = v[i]; 59 | if (buff_len + num_bits <= 64) 60 | { 61 | buff |= (x & val_mask) << buff_len; 62 | buff_len += num_bits; 63 | } 64 | else 65 | { 66 | assert(num_bits > 56); 67 | buff |= (x & 0xFF) << buff_len; 68 | res.push_back(buff & 0xFF); 69 | buff >>= 8; 70 | x >>= 8; 71 | buff |= (x & (val_mask >> 8)) << buff_len; 72 | buff_len += num_bits - 8; 73 | } 74 | } 75 | while (buff_len >= 8) 76 | { 77 | res.push_back(buff & 0xFF); 78 | buff >>= 8; 79 | buff_len -= 8; 80 | } 81 | if (buff_len > 0) 82 | { 83 | res.push_back(buff & 0xFF); 84 | } 85 | return std::make_pair(std::move(res), std::move(res_params)); 86 | } // encode() 87 | 88 | template < typename Int_Type > 89 | std::vector< Int_Type > 90 | decode(Code_Type const & v, Code_Params_Type const & v_params) const 91 | { 92 | std::vector< Int_Type > res; 93 | unsigned num_bits; 94 | size_t sz; 95 | std::istringstream(v_params.at("num_bits")) >> num_bits; 96 | std::istringstream(v_params.at("size")) >> sz; 97 | if (v.size() != (sz * num_bits) / 8 + ((sz * num_bits) % 8 > 0? 1 : 0)) 98 | { 99 | LOG_THROW 100 | << "incorrect size: v_size=" << v.size(); 101 | } 102 | long long unsigned buff = 0; 103 | unsigned buff_len = 0; 104 | unsigned j = 0; 105 | auto val_mask = (1llu << num_bits) - 1; 106 | for (unsigned i = 0; i < sz; ++i) 107 | { 108 | while (j < v.size() and buff_len <= 64 - 8) 109 | { 110 | buff |= ((long long unsigned)v.at(j) << buff_len); 111 | ++j; 112 | buff_len += 8; 113 | } 114 | long long unsigned x; 115 | if (buff_len >= num_bits) 116 | { 117 | x = buff & val_mask; 118 | buff >>= num_bits; 119 | buff_len -= num_bits; 120 | } 121 | else 122 | { 123 | // 56 < buff_len < num_bits 124 | x = buff & 0xFF; 125 | buff >>= 8; 126 | buff_len -= 8; 127 | buff |= (v.at(j) << buff_len); 128 | ++j; 129 | buff_len += 8; 130 | x |= ((buff & (val_mask >> 8)) << 8); 131 | buff >>= (num_bits - 8); 132 | buff_len -= num_bits - 8; 133 | } 134 | res.push_back(x); 135 | } 136 | return res; 137 | } // decode() 138 | 139 | // 140 | // static packer access 141 | // 142 | static Bit_Packer const & 143 | get_packer() 144 | { 145 | static Bit_Packer _packer; 146 | return _packer; 147 | } 148 | }; // class Bit_Packer 149 | 150 | } // namespace fast5 151 | 152 | #endif 153 | -------------------------------------------------------------------------------- /SATnano/build/lib/Makefile: -------------------------------------------------------------------------------- 1 | # CMAKE generated file: DO NOT EDIT! 2 | # Generated by "Unix Makefiles" Generator, CMake Version 2.6 3 | 4 | # Default target executed when no arguments are given to make. 5 | default_target: all 6 | .PHONY : default_target 7 | 8 | #============================================================================= 9 | # Special targets provided by cmake. 10 | 11 | # Disable implicit rules so canoncical targets will work. 12 | .SUFFIXES: 13 | 14 | # Remove some rules from gmake that .SUFFIXES does not remove. 15 | SUFFIXES = 16 | 17 | .SUFFIXES: .hpux_make_needs_suffix_list 18 | 19 | # Suppress display of executed commands. 20 | $(VERBOSE).SILENT: 21 | 22 | # A target that is always out of date. 23 | cmake_force: 24 | .PHONY : cmake_force 25 | 26 | #============================================================================= 27 | # Set environment variables for the build. 28 | 29 | # The shell in which to execute make rules. 30 | SHELL = /bin/sh 31 | 32 | # The CMake executable. 33 | CMAKE_COMMAND = /usr/bin/cmake 34 | 35 | # The command to remove a file. 36 | RM = /usr/bin/cmake -E remove -f 37 | 38 | # The program to use to edit the cache. 39 | CMAKE_EDIT_COMMAND = /usr/bin/ccmake 40 | 41 | # The top-level source directory on which CMake was run. 42 | CMAKE_SOURCE_DIR = /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano 43 | 44 | # The top-level build 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#============================================================================= 114 | # Special targets to cleanup operation of make. 115 | 116 | # Special rule to run CMake to check the build system integrity. 117 | # No rule that depends on this can have commands that come from listfiles 118 | # because they might be regenerated. 119 | cmake_check_build_system: 120 | cd /mnt/hgfs/data/projects/cwdtw-fastalign/data/cwSDTWnano/SATnano/build && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0 121 | .PHONY : cmake_check_build_system 122 | 123 | -------------------------------------------------------------------------------- /SATnano/build/src/Makefile: -------------------------------------------------------------------------------- 1 | # CMAKE generated file: DO NOT EDIT! 2 | # Generated by "Unix Makefiles" Generator, CMake Version 2.6 3 | 4 | # Default target executed when no arguments are given to make. 5 | default_target: all 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