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stage 4 & 5 changed according to previous changes

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maheydari committed Aug 18, 2015
0 parents commit f20971fedb38d564813d29a334e1794430a42836
Showing with 56,735 additions and 0 deletions.
  1. +75 −0 CMakeLists.txt
  2. +340 −0 LICENSE
  3. +2 −0 README.md
  4. +4 −0 brownie.kdev4
  5. +131 −0 cmake/FindGSL.cmake
  6. +23 −0 cmake/FindSparseHash.cmake
  7. +16 −0 scripts/distribute
  8. +12 −0 src/CMakeLists.txt
  9. +396 −0 src/alignment.cpp
  10. +59 −0 src/alignment.h
  11. +113 −0 src/arc.h
  12. +390 −0 src/brownie.cpp
  13. +169 −0 src/brownie.h
  14. +524 −0 src/bubble.cpp
  15. +272 −0 src/cliptips.cpp
  16. +854 −0 src/correction.cpp
  17. +1,317 −0 src/coverage.cpp
  18. +258 −0 src/dbperm.cpp
  19. +66 −0 src/dsnode.cpp
  20. +580 −0 src/dsnode.h
  21. +1 −0 src/essaMEM-master/CMakeLists.txt
  22. +24 −0 src/essaMEM-master/LICENSE
  23. +109 −0 src/essaMEM-master/fasta.cpp
  24. +14 −0 src/essaMEM-master/fasta.hpp
  25. +23 −0 src/essaMEM-master/license.txt
  26. +1 −0 src/essaMEM-master/lock.txt
  27. +387 −0 src/essaMEM-master/mummer.cpp
  28. +303 −0 src/essaMEM-master/qsufsort.c
  29. +49 −0 src/essaMEM-master/readme.txt
  30. +885 −0 src/essaMEM-master/sparseSA.cpp
  31. +233 −0 src/essaMEM-master/sparseSA.hpp
  32. +130 −0 src/fasta.cpp
  33. +35 −0 src/fasta.hpp
  34. +1 −0 src/fiblib/CMakeLists.txt
  35. +696 −0 src/fiblib/fib.c
  36. +74 −0 src/fiblib/fib.h
  37. +106 −0 src/fiblib/fibheap.h
  38. +98 −0 src/fiblib/fibpriv.h
  39. +247 −0 src/fiblib/msstdint.h
  40. +24 −0 src/gaussval.cpp
  41. +227 −0 src/gaussval.h
  42. +128 −0 src/global.h
  43. +1,045 −0 src/graph.cpp
  44. +591 −0 src/graph.h
  45. +247 −0 src/kmernode.cpp
  46. +350 −0 src/kmernode.h
  47. +461 −0 src/kmeroverlap.cpp
  48. +638 −0 src/kmeroverlap.h
  49. +446 −0 src/kmertable.cpp
  50. +198 −0 src/kmertable.h
  51. +380 −0 src/library.cpp
  52. +856 −0 src/library.h
  53. +47 −0 src/nodeendstable.cpp
  54. +152 −0 src/nodeendstable.h
  55. +301 −0 src/nodenbh.h
  56. +103 −0 src/nucleotide.cpp
  57. +248 −0 src/nucleotide.h
  58. +29 −0 src/observations.cpp
  59. +119 −0 src/observations.h
  60. +109 −0 src/perm.cpp
  61. +303 −0 src/qsufsort.c
  62. +1 −0 src/readfile/CMakeLists.txt
  63. +67 −0 src/readfile/fastafile.cpp
  64. +54 −0 src/readfile/fastafile.h
  65. +67 −0 src/readfile/fastqfile.cpp
  66. +57 −0 src/readfile/fastqfile.h
  67. +74 −0 src/readfile/fstream_ts.cpp
  68. +166 −0 src/readfile/fstream_ts.h
  69. +52 −0 src/readfile/rawfile.cpp
  70. +54 −0 src/readfile/rawfile.h
  71. +105 −0 src/readfile/readfile.cpp
  72. +427 −0 src/readfile/readfile.h
  73. +59 −0 src/readfile/samfile.cpp
  74. +53 −0 src/readfile/samfile.h
  75. +54 −0 src/readfile/sequencefile.cpp
  76. +54 −0 src/readfile/sequencefile.h
  77. +445 −0 src/readmap.cpp
  78. +415 −0 src/reductions.cpp
  79. +354 −0 src/scaffold.cpp
  80. +184 −0 src/settings.cpp
  81. +144 −0 src/settings.h
  82. +661 −0 src/solutioncomp.cpp
  83. +885 −0 src/sparseSA.cpp
  84. +233 −0 src/sparseSA.hpp
  85. +608 −0 src/ssnode.h
  86. +1,246 −0 src/suffix_tree.c
  87. +166 −0 src/suffix_tree.h
  88. +892 −0 src/tkmer.h
  89. +292 −0 src/tstring.cpp
  90. +432 −0 src/tstring.h
  91. +85 −0 src/util.cpp
  92. +69 −0 src/util.h
  93. +14 −0 unittest/CMakeLists.txt
  94. +63 −0 unittest/fibtest.cpp
  95. +130 −0 unittest/gtest/CHANGES
  96. +240 −0 unittest/gtest/CMakeLists.txt
  97. +37 −0 unittest/gtest/CONTRIBUTORS
  98. +28 −0 unittest/gtest/COPYING
  99. +424 −0 unittest/gtest/README
  100. +216 −0 unittest/gtest/cmake/internal_utils.cmake
  101. +283 −0 unittest/gtest/include/gtest/gtest-death-test.h
  102. +230 −0 unittest/gtest/include/gtest/gtest-message.h
  103. +1,421 −0 unittest/gtest/include/gtest/gtest-param-test.h
  104. +487 −0 unittest/gtest/include/gtest/gtest-param-test.h.pump
  105. +796 −0 unittest/gtest/include/gtest/gtest-printers.h
  106. +232 −0 unittest/gtest/include/gtest/gtest-spi.h
  107. +176 −0 unittest/gtest/include/gtest/gtest-test-part.h
  108. +259 −0 unittest/gtest/include/gtest/gtest-typed-test.h
  109. +2,155 −0 unittest/gtest/include/gtest/gtest.h
  110. +358 −0 unittest/gtest/include/gtest/gtest_pred_impl.h
  111. +58 −0 unittest/gtest/include/gtest/gtest_prod.h
  112. +308 −0 unittest/gtest/include/gtest/internal/gtest-death-test-internal.h
  113. +210 −0 unittest/gtest/include/gtest/internal/gtest-filepath.h
  114. +1,226 −0 unittest/gtest/include/gtest/internal/gtest-internal.h
  115. +233 −0 unittest/gtest/include/gtest/internal/gtest-linked_ptr.h
  116. +4,822 −0 unittest/gtest/include/gtest/internal/gtest-param-util-generated.h
  117. +301 −0 unittest/gtest/include/gtest/internal/gtest-param-util-generated.h.pump
  118. +619 −0 unittest/gtest/include/gtest/internal/gtest-param-util.h
  119. +1,775 −0 unittest/gtest/include/gtest/internal/gtest-port.h
  120. +350 −0 unittest/gtest/include/gtest/internal/gtest-string.h
  121. +968 −0 unittest/gtest/include/gtest/internal/gtest-tuple.h
  122. +336 −0 unittest/gtest/include/gtest/internal/gtest-tuple.h.pump
  123. +3,330 −0 unittest/gtest/include/gtest/internal/gtest-type-util.h
  124. +296 −0 unittest/gtest/include/gtest/internal/gtest-type-util.h.pump
  125. +48 −0 unittest/gtest/src/gtest-all.cc
  126. +1,234 −0 unittest/gtest/src/gtest-death-test.cc
  127. +380 −0 unittest/gtest/src/gtest-filepath.cc
  128. +1,038 −0 unittest/gtest/src/gtest-internal-inl.h
  129. +746 −0 unittest/gtest/src/gtest-port.cc
  130. +356 −0 unittest/gtest/src/gtest-printers.cc
  131. +110 −0 unittest/gtest/src/gtest-test-part.cc
  132. +110 −0 unittest/gtest/src/gtest-typed-test.cc
  133. +4,898 −0 unittest/gtest/src/gtest.cc
  134. +39 −0 unittest/gtest/src/gtest_main.cc
  135. +24 −0 unittest/kmermdtest.cpp
  136. +239 −0 unittest/kmertest.cpp
  137. +63 −0 unittest/nucleotidetest.cpp
  138. +252 −0 unittest/readfiletest.cpp
  139. +116 −0 unittest/scaffoldtest.cpp
  140. +31 −0 unittest/test.fa
  141. BIN unittest/test.fa.gz
  142. +36 −0 unittest/test.fastq
  143. BIN unittest/test.fastq.gz
  144. +10 −0 unittest/test.raw
  145. BIN unittest/test.raw.gz
  146. +10 −0 unittest/test.sam
  147. BIN unittest/test.sam.gz
  148. +137 −0 unittest/tstringtest.cpp
  149. BIN unittest/unittest
  150. +3 −0 unittest/valgrind.sh
@@ -0,0 +1,75 @@
# CMake compatibility issues: don't modify this, please!
cmake_minimum_required(VERSION 2.6.3)
project(brownie)
# project version
set(${PROJECT_NAME}_MAJOR_VERSION 0)
set(${PROJECT_NAME}_MINOR_VERSION 1)
set(${PROJECT_NAME}_PATCH_LEVEL 0)
# set the default configuration to Release
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release" CACHE STRING
"Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel." FORCE)
endif(NOT CMAKE_BUILD_TYPE)
# set the module path
set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
# set some definitions
add_definitions("-DMAXKMERLENGTH=31")
add_definitions("-DCATEGORIES=2")
add_definitions("-DBROWNIE_MAJOR_VERSION=${${PROJECT_NAME}_MAJOR_VERSION}")
add_definitions("-DBROWNIE_MINOR_VERSION=${${PROJECT_NAME}_MINOR_VERSION}")
add_definitions("-DBROWNIE_PATCH_LEVEL=${${PROJECT_NAME}_PATCH_LEVEL}")
# set windows specific flags
if (MSVC)
add_definitions("-D_SCL_SECURE_NO_WARNINGS")
add_definitions("-D_CRT_SECURE_NO_WARNINGS")
endif (MSVC)
# set g++ specific flags
if (CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_GNUCC)
set(CMAKE_CXX_FLAGS "-Wno-deprecated -std=c++11 -static-libgcc -static-libstdc++")
set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g3 -Wall -pedantic -Wno-long-long")
set(CMAKE_CXX_FLAGS_RELEASE "-O3")
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -g3")
set(CMAKE_C_FLAGS_DEBUG "-O0 -g3 -Wall -pedantic -Wno-long-long")
endif (CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_GNUCC)
# uncomment the portion below to disable assertions
if (CMAKE_BUILD_TYPE STREQUAL Release)
# add_definitions(-DNDEBUG)
endif (CMAKE_BUILD_TYPE STREQUAL Release)
# check if zlib is present
find_package(ZLIB)
if (ZLIB_FOUND)
add_definitions(-DHAVE_ZLIB)
include_directories(${ZLIB_INCLUDE_DIR})
endif(ZLIB_FOUND)
# check if gsl is present
find_package(GSL REQUIRED)
include_directories(${GSL_INCLUDE_DIR})
set(CMAKE_VERBOSE_MAKEFILE ON)
# set include path for Google's sparse hash table
find_package(SparseHash)
if (SPARSEHASH_FOUND)
include_directories(${SPARSEHASH_INCLUDE_DIR})
else (SPARSEHASH_FOUND)
message(FATAL_ERROR "\nFATAL ERROR: The required Google SparseHash package"
" could not be found on this system. Please refer to the Velvet "
"manual for the Google Sparsehash installation instructions. If "
"you installed Google Sparsehash in a non-standard location "
"(e.g. somewhere in your homedir), you can point cmake to the "
"installation location as follows: \ncmake "
"-DSPARSEHASH_INCLUDE_DIR=<path-to-sparsehash>/include .")
endif(SPARSEHASH_FOUND)
add_subdirectory(src)
add_subdirectory(unittest)
340 LICENSE

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@@ -0,0 +1,2 @@
# brownie
Brownie
@@ -0,0 +1,4 @@
[Project]
Name=brownie
Manager=KDevCMakeManager
VersionControl=kdevgit
@@ -0,0 +1,131 @@
##
## Try to find gnu scientific library GSL
## (see http://www.gnu.org/software/gsl/)
## Once run this will define:
##
## GSL_FOUND = system has GSL lib
##
## GSL_LIBRARIES = full path to the libraries
## on Unix/Linux with additional linker flags from "gsl-config --libs"
##
## CMAKE_GSL_CXX_FLAGS = Unix compiler flags for GSL, essentially "`gsl-config --cxxflags`"
##
## GSL_INCLUDE_DIR = where to find headers
##
## GSL_LINK_DIRECTORIES = link directories, useful for rpath on Unix
## GSL_EXE_LINKER_FLAGS = rpath on Unix
##
## Felix Woelk 07/2004
## minor corrections Jan Woetzel
##
## www.mip.informatik.uni-kiel.de
## --------------------------------
##
IF(WIN32)
SET(GSL_MINGW_PREFIX "c:/msys/local" )
SET(GSL_MSVC_PREFIX "$ENV{LIB_DIR}")
FIND_LIBRARY(GSL_LIB gsl PATHS
${GSL_MINGW_PREFIX}/lib
${GSL_MSVC_PREFIX}/lib
)
#MSVC version of the lib is just called 'cblas'
FIND_LIBRARY(GSLCBLAS_LIB gslcblas cblas PATHS
${GSL_MINGW_PREFIX}/lib
${GSL_MSVC_PREFIX}/lib
)
FIND_PATH(GSL_INCLUDE_DIR gsl/gsl_blas.h
${GSL_MINGW_PREFIX}/include
${GSL_MSVC_PREFIX}/include
)
IF (GSL_LIB AND GSLCBLAS_LIB)
SET (GSL_LIBRARIES ${GSL_LIB} ${GSLCBLAS_LIB})
ENDIF (GSL_LIB AND GSLCBLAS_LIB)
ELSE(WIN32)
IF(UNIX)
SET(GSL_CONFIG_PREFER_PATH "$ENV{GSL_HOME}/bin" CACHE STRING "preferred path to GSL (gsl-config)")
FIND_PROGRAM(GSL_CONFIG gsl-config
${GSL_CONFIG_PREFER_PATH}
$ENV{LIB_DIR}/bin
/usr/local/bin/
/usr/bin/
)
# MESSAGE("DBG GSL_CONFIG ${GSL_CONFIG}")
IF (GSL_CONFIG)
# set CXXFLAGS to be fed into CXX_FLAGS by the user:
SET(GSL_CXX_FLAGS "`${GSL_CONFIG} --cflags`")
# set INCLUDE_DIRS to prefix+include
EXEC_PROGRAM(${GSL_CONFIG}
ARGS --prefix
OUTPUT_VARIABLE GSL_PREFIX)
SET(GSL_INCLUDE_DIR ${GSL_PREFIX}/include CACHE STRING INTERNAL)
# set link libraries and link flags
EXEC_PROGRAM(${GSL_CONFIG}
ARGS --libs
OUTPUT_VARIABLE GSL_LIBRARIES)
## extract link dirs for rpath
EXEC_PROGRAM(${GSL_CONFIG}
ARGS --libs
OUTPUT_VARIABLE GSL_CONFIG_LIBS )
## split off the link dirs (for rpath)
## use regular expression to match wildcard equivalent "-L*<endchar>"
## with <endchar> is a space or a semicolon
STRING(REGEX MATCHALL "[-][L]([^ ;])+"
GSL_LINK_DIRECTORIES_WITH_PREFIX
"${GSL_CONFIG_LIBS}" )
# MESSAGE("DBG GSL_LINK_DIRECTORIES_WITH_PREFIX=${GSL_LINK_DIRECTORIES_WITH_PREFIX}")
## remove prefix -L because we need the pure directory for LINK_DIRECTORIES
IF (GSL_LINK_DIRECTORIES_WITH_PREFIX)
STRING(REGEX REPLACE "[-][L]" "" GSL_LINK_DIRECTORIES ${GSL_LINK_DIRECTORIES_WITH_PREFIX} )
ENDIF (GSL_LINK_DIRECTORIES_WITH_PREFIX)
SET(GSL_EXE_LINKER_FLAGS "-Wl,-rpath,${GSL_LINK_DIRECTORIES}" CACHE STRING INTERNAL)
# MESSAGE("DBG GSL_LINK_DIRECTORIES=${GSL_LINK_DIRECTORIES}")
# MESSAGE("DBG GSL_EXE_LINKER_FLAGS=${GSL_EXE_LINKER_FLAGS}")
# ADD_DEFINITIONS("-DHAVE_GSL")
# SET(GSL_DEFINITIONS "-DHAVE_GSL")
MARK_AS_ADVANCED(
GSL_CXX_FLAGS
GSL_INCLUDE_DIR
GSL_LIBRARIES
GSL_LINK_DIRECTORIES
GSL_DEFINITIONS
)
ELSE(GSL_CONFIG)
IF (GSL_FIND_REQUIRED)
MESSAGE(FATAL_ERROR "Could not find gsl-config. Please set it manually. GSL_CONFIG=${GSL_CONFIG}")
ELSE (GSL_FIND_REQUIRED)
MESSAGE(STATUS "Could not find GSL")
# TODO: Avoid cmake complaints if GSL is not found
ENDIF (GSL_FIND_REQUIRED)
ENDIF(GSL_CONFIG)
ENDIF(UNIX)
ENDIF(WIN32)
IF(GSL_LIBRARIES)
IF(GSL_INCLUDE_DIR OR GSL_CXX_FLAGS)
SET(GSL_FOUND 1)
MESSAGE(STATUS "Using GSL from ${GSL_PREFIX}")
ENDIF(GSL_INCLUDE_DIR OR GSL_CXX_FLAGS)
ENDIF(GSL_LIBRARIES)
@@ -0,0 +1,23 @@
# This file was borrowed from the pcsx2 - a Playstation 2 Emulator project.
# No header was provided with this file, nor was there a licence file.
# If anyone thinks that the use of this file violates certain copyrights,
# please inform me of this matter. - Jan Fostier, May 12 2011.
# Try to find SparseHash
# Once done, this will define
#
# SPARSEHASH_FOUND - system has SparseHash
# SPARSEHASH_INCLUDE_DIR - the SparseHash include directories
if(SPARSEHASH_INCLUDE_DIR)
set(SPARSEHASH_FIND_QUIETLY TRUE)
endif(SPARSEHASH_INCLUDE_DIR)
find_path(SPARSEHASH_INCLUDE_DIR google/sparsehash/sparsehashtable.h)
# handle the QUIETLY and REQUIRED arguments and set SPARSEHASH_FOUND to TRUE if
# all listed variables are TRUE
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(SparseHash DEFAULT_MSG SPARSEHASH_INCLUDE_DIR)
mark_as_advanced(SPARSEHASH_INCLUDE_DIR)
@@ -0,0 +1,16 @@
#/bin/sh!
version=0.1
cd ..
mkdir brownie-"$version"
cd brownie-"$version"
# cp ../README .
# cp ../INSTALL .
cp ../CMakeLists.txt .
find ../src | grep -v '/\.' | grep -v [~] | cpio -dump src
find ../unittest | grep -v '/\.' | grep -v [~] | cpio -dump unittest
find ../cmake | grep -v '/\.' | grep -v [~] | cpio -dump cmake
cd ..
tar -czf brownie-"$version".tar.gz brownie-"$version"
rm -r -f brownie-"$version"
echo "Done!"
@@ -0,0 +1,12 @@
add_executable(brownie alignment.cpp gaussval.cpp observations.cpp reductions.cpp correction.cpp bubble.cpp coverage.cpp library.cpp kmernode.cpp kmertable.cpp cliptips.cpp dsnode.cpp nucleotide.cpp nodeendstable.cpp settings.cpp util.cpp tstring.cpp kmeroverlap.cpp graph.cpp brownie.cpp solutioncomp.cpp suffix_tree.c)
target_link_libraries(brownie fiblib readfile essaMEM ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} ${GSL_LIBRARIES} pthread)
if (ZLIB_FOUND)
target_link_libraries(brownie ${ZLIB_LIBRARY})
endif (ZLIB_FOUND)
install(TARGETS brownie RUNTIME DESTINATION bin)
add_subdirectory(readfile)
add_subdirectory(fiblib)
add_subdirectory(essaMEM-master)
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