<commit_before>#seqan
if (USE_SEQAN)
  message(STATUS "using seqan" )
  include_directories("${OPT_DIR}/seqan/include")
  set( SEQAN_FLAGS "-DSEQAN_ENABLE_DEBUG=0 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP=1 -DSEQAN_HAS_ZLIB=1" )
  set( SEQAN_FLAGS "${SEQAN_FLAGS} -W -Wall -Wno-long-long -pedantic -Wno-variadic-macros" )

  set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_FLAGS}" )
  set( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lbz2 -lz" )
endif (USE_SEQAN)

#boost
ADD_DEFINITIONS(-DBOOST_LOG_DYN_LINK)

#automatically discover modules/<name> and compile modules/<name>/main.cpp into a library named <name>
include(modules/modules.cmake)

set (EXTRA_LIBS ${EXTRA_LIBS} boost_program_options boost_log )

add_library( allpathslg
    ${OPT_DIR}/allpathslg/src/CompressedSequence.cc
    ${OPT_DIR}/allpathslg/src/TokenizeString.cc
    ${OPT_DIR}/allpathslg/src/Equiv.cc
    ${OPT_DIR}/allpathslg/src/FastIfstream.cc
    ${OPT_DIR}/allpathslg/src/FastaConverter.cc
    ${OPT_DIR}/allpathslg/src/FastaFileset.cc
    ${OPT_DIR}/allpathslg/src/FastaFilestream.cc
    ${OPT_DIR}/allpathslg/src/FastaFilestreamPreview.cc
    ${OPT_DIR}/allpathslg/src/FastaVerifier.cc
    ${OPT_DIR}/allpathslg/src/FastaNameParser.cc
    ${OPT_DIR}/allpathslg/src/Fastavector.cc
    ${OPT_DIR}/allpathslg/src/PackAlign.cc
    ${OPT_DIR}/allpathslg/src/PrintAlignment.cc
    ${OPT_DIR}/allpathslg/src/Vec.cc
    ${OPT_DIR}/allpathslg/src/dna/Bases.cc
    ${OPT_DIR}/allpathslg/src/feudal/BaseVec.cc
    ${OPT_DIR}/allpathslg/src/feudal/FeudalFileReader.cc
    ${OPT_DIR}/allpathslg/src/feudal/FeudalFileWriter.cc
    ${OPT_DIR}/allpathslg/src/feudal/FeudalControlBlock.cc
    ${OPT_DIR}/allpathslg/src/feudal/Mempool.cc
    ${OPT_DIR}/allpathslg/src/feudal/Generic.cc
    ${OPT_DIR}/allpathslg/src/feudal/BitVec.cc
    ${OPT_DIR}/allpathslg/src/feudal/Oob.cc
    ${OPT_DIR}/allpathslg/src/feudal/CharString.cc
    ${OPT_DIR}/allpathslg/src/feudal/BinaryStream.cc
    ${OPT_DIR}/allpathslg/src/graph/Digraph.cc
    ${OPT_DIR}/allpathslg/src/math/Matrix.cc
    ${OPT_DIR}/allpathslg/src/math/Permutation.cc
    ${OPT_DIR}/allpathslg/src/random/RNGen.cc
    ${OPT_DIR}/allpathslg/src/pairwise_aligners/SmithWatFree.cc
    ${OPT_DIR}/allpathslg/src/pairwise_aligners/SmithWatBandedA.cc
    ${OPT_DIR}/allpathslg/src/system/file/Directory.cc
    ${OPT_DIR}/allpathslg/src/system/file/FileReader.cc
    ${OPT_DIR}/allpathslg/src/system/file/SymLink.cc
    ${OPT_DIR}/allpathslg/src/system/file/File.cc
    ${OPT_DIR}/allpathslg/src/system/file/FileWriter.cc
    ${OPT_DIR}/allpathslg/src/system/file/TempFile.cc
    ${OPT_DIR}/allpathslg/src/system/AllOfOutput.cc
    ${OPT_DIR}/allpathslg/src/system/HostName.cc
    ${OPT_DIR}/allpathslg/src/system/ParallelSortTest.cc
    ${OPT_DIR}/allpathslg/src/system/System.cc
    ${OPT_DIR}/allpathslg/src/system/UseGDB.cc
    ${OPT_DIR}/allpathslg/src/system/Assert.cc
    ${OPT_DIR}/allpathslg/src/system/HTMLUtils.cc
    ${OPT_DIR}/allpathslg/src/system/ParsedArgs.cc
    ${OPT_DIR}/allpathslg/src/system/Utils.cc
    ${OPT_DIR}/allpathslg/src/system/Crash.cc
    ${OPT_DIR}/allpathslg/src/system/MemTracker.cc
    ${OPT_DIR}/allpathslg/src/system/ProcBuf.cc
    ${OPT_DIR}/allpathslg/src/system/WorklistMP.cc
    ${OPT_DIR}/allpathslg/src/system/ErrNo.cc
    ${OPT_DIR}/allpathslg/src/system/MiscUtil.cc
    ${OPT_DIR}/allpathslg/src/system/RunTime.cc
    ${OPT_DIR}/allpathslg/src/system/TraceVal.cc
    ${OPT_DIR}/allpathslg/src/system/WorklistUtils.cc
    ${OPT_DIR}/allpathslg/src/system/Exit.cc
    ${OPT_DIR}/allpathslg/src/system/Parallel.cc
    ${OPT_DIR}/allpathslg/src/system/SysConf.cc
    ${OPT_DIR}/allpathslg/src/system/Types.cc
    ${OPT_DIR}/allpathslg/src/system/Thread.cc
    ${OPT_DIR}/allpathslg/src/system/ThreadsafeIO.cc
    )
set (EXTRA_LIBS ${EXTRA_LIBS} allpathslg)

add_executable(ccbb ccbb.cpp)
add_dependencies(ccbb buildinfo)
if(TARGET boost)
  add_dependencies(ccbb boost)
endif(TARGET boost)
target_link_libraries(ccbb ${EXTRA_LIBS})

install (TARGETS ccbb DESTINATION bin)<commit_msg>added a hook to add extra cmake instruction without changing this repo<commit_after>#seqan
if (USE_SEQAN)
  message(STATUS "using seqan" )
  include_directories("${OPT_DIR}/seqan/include")
  set( SEQAN_FLAGS "-DSEQAN_ENABLE_DEBUG=0 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_HAS_BZIP=1 -DSEQAN_HAS_ZLIB=1" )
  set( SEQAN_FLAGS "${SEQAN_FLAGS} -W -Wall -Wno-long-long -pedantic -Wno-variadic-macros" )

  set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_FLAGS}" )
  set( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lbz2 -lz" )
endif (USE_SEQAN)

#boost
ADD_DEFINITIONS(-DBOOST_LOG_DYN_LINK)

#automatically discover modules/<name> and compile modules/<name>/main.cpp into a library named <name>
include(modules/modules.cmake)

set (EXTRA_LIBS ${EXTRA_LIBS} boost_program_options boost_log )

if (EXISTS ${SRC_DIR}/modules/extra.cmake)
  include(${SRC_DIR}/modules/extra.cmake)
endif (EXISTS ${SRC_DIR}/modules/extra.cmake)

add_library( allpathslg
    ${OPT_DIR}/allpathslg/src/CompressedSequence.cc
    ${OPT_DIR}/allpathslg/src/TokenizeString.cc
    ${OPT_DIR}/allpathslg/src/Equiv.cc
    ${OPT_DIR}/allpathslg/src/FastIfstream.cc
    ${OPT_DIR}/allpathslg/src/FastaConverter.cc
    ${OPT_DIR}/allpathslg/src/FastaFileset.cc
    ${OPT_DIR}/allpathslg/src/FastaFilestream.cc
    ${OPT_DIR}/allpathslg/src/FastaFilestreamPreview.cc
    ${OPT_DIR}/allpathslg/src/FastaVerifier.cc
    ${OPT_DIR}/allpathslg/src/FastaNameParser.cc
    ${OPT_DIR}/allpathslg/src/Fastavector.cc
    ${OPT_DIR}/allpathslg/src/PackAlign.cc
    ${OPT_DIR}/allpathslg/src/PrintAlignment.cc
    ${OPT_DIR}/allpathslg/src/Vec.cc
    ${OPT_DIR}/allpathslg/src/dna/Bases.cc
    ${OPT_DIR}/allpathslg/src/feudal/BaseVec.cc
    ${OPT_DIR}/allpathslg/src/feudal/FeudalFileReader.cc
    ${OPT_DIR}/allpathslg/src/feudal/FeudalFileWriter.cc
    ${OPT_DIR}/allpathslg/src/feudal/FeudalControlBlock.cc
    ${OPT_DIR}/allpathslg/src/feudal/Mempool.cc
    ${OPT_DIR}/allpathslg/src/feudal/Generic.cc
    ${OPT_DIR}/allpathslg/src/feudal/BitVec.cc
    ${OPT_DIR}/allpathslg/src/feudal/Oob.cc
    ${OPT_DIR}/allpathslg/src/feudal/CharString.cc
    ${OPT_DIR}/allpathslg/src/feudal/BinaryStream.cc
    ${OPT_DIR}/allpathslg/src/graph/Digraph.cc
    ${OPT_DIR}/allpathslg/src/math/Matrix.cc
    ${OPT_DIR}/allpathslg/src/math/Permutation.cc
    ${OPT_DIR}/allpathslg/src/random/RNGen.cc
    ${OPT_DIR}/allpathslg/src/pairwise_aligners/SmithWatFree.cc
    ${OPT_DIR}/allpathslg/src/pairwise_aligners/SmithWatBandedA.cc
    ${OPT_DIR}/allpathslg/src/system/file/Directory.cc
    ${OPT_DIR}/allpathslg/src/system/file/FileReader.cc
    ${OPT_DIR}/allpathslg/src/system/file/SymLink.cc
    ${OPT_DIR}/allpathslg/src/system/file/File.cc
    ${OPT_DIR}/allpathslg/src/system/file/FileWriter.cc
    ${OPT_DIR}/allpathslg/src/system/file/TempFile.cc
    ${OPT_DIR}/allpathslg/src/system/AllOfOutput.cc
    ${OPT_DIR}/allpathslg/src/system/HostName.cc
    ${OPT_DIR}/allpathslg/src/system/ParallelSortTest.cc
    ${OPT_DIR}/allpathslg/src/system/System.cc
    ${OPT_DIR}/allpathslg/src/system/UseGDB.cc
    ${OPT_DIR}/allpathslg/src/system/Assert.cc
    ${OPT_DIR}/allpathslg/src/system/HTMLUtils.cc
    ${OPT_DIR}/allpathslg/src/system/ParsedArgs.cc
    ${OPT_DIR}/allpathslg/src/system/Utils.cc
    ${OPT_DIR}/allpathslg/src/system/Crash.cc
    ${OPT_DIR}/allpathslg/src/system/MemTracker.cc
    ${OPT_DIR}/allpathslg/src/system/ProcBuf.cc
    ${OPT_DIR}/allpathslg/src/system/WorklistMP.cc
    ${OPT_DIR}/allpathslg/src/system/ErrNo.cc
    ${OPT_DIR}/allpathslg/src/system/MiscUtil.cc
    ${OPT_DIR}/allpathslg/src/system/RunTime.cc
    ${OPT_DIR}/allpathslg/src/system/TraceVal.cc
    ${OPT_DIR}/allpathslg/src/system/WorklistUtils.cc
    ${OPT_DIR}/allpathslg/src/system/Exit.cc
    ${OPT_DIR}/allpathslg/src/system/Parallel.cc
    ${OPT_DIR}/allpathslg/src/system/SysConf.cc
    ${OPT_DIR}/allpathslg/src/system/Types.cc
    ${OPT_DIR}/allpathslg/src/system/Thread.cc
    ${OPT_DIR}/allpathslg/src/system/ThreadsafeIO.cc
    )
set (EXTRA_LIBS ${EXTRA_LIBS} allpathslg)


add_executable(ccbb ccbb.cpp)
add_dependencies(ccbb buildinfo)
if(TARGET boost)
  add_dependencies(ccbb boost)
endif(TARGET boost)
target_link_libraries(ccbb ${EXTRA_LIBS})

install (TARGETS ccbb DESTINATION bin)
{'fraction_non_alphanumeric': 0.1471725471242146, 'fraction_numerical': 0.001208313194780087, 'mean_word_length': 4.532754010695188, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2085159', 'n_tokens_mistral': 3449, 'n_tokens_neox': 3394, 'n_words': 287}