Here is a list of all file members with links to the files they belong to:

- a -

• aligner_capabilities_t : capabilities.hpp
• ALIGNER_STATISTICS : Job.hpp
• ALIGNMENT_METHOD_GLOBAL : Constants.hpp
• ALIGNMENT_METHOD_LOCAL : Constants.hpp
• alignPartition() : sw_stage1.cpp
• ALL_STAGES : libmasa.cpp
• ARG_ALIGNMENT_EDGES : libmasa.cpp
• ARG_ALIGNMENT_END : libmasa.cpp
• ARG_ALIGNMENT_ID : libmasa.cpp
• ARG_ALIGNMENT_START : libmasa.cpp
• ARG_BLOCK_HEIGHT : BlockAlignerParameters.cpp
• ARG_BLOCK_SIZE : BlockAlignerParameters.cpp
• ARG_BLOCK_WIDTH : BlockAlignerParameters.cpp
• ARG_CLEAR : libmasa.cpp
• ARG_CLEAR_N : libmasa.cpp
• ARG_COMPLEMENT : libmasa.cpp
• ARG_DISK_SIZE : libmasa.cpp
• ARG_DRAW_PRUNING : libmasa.cpp
• ARG_DUMP_BLOCKS : libmasa.cpp
• ARG_FLUSH_COLUMN : libmasa.cpp
• ARG_FORK : libmasa.cpp
• ARG_GRID_HEIGHT : BlockAlignerParameters.cpp
• ARG_GRID_SIZE : BlockAlignerParameters.cpp
• ARG_GRID_WIDTH : BlockAlignerParameters.cpp
• ARG_HELP : libmasa.cpp
• ARG_LIST_FORMATS : libmasa.cpp
• ARG_LOAD_COLUMN : libmasa.cpp
• ARG_MASANET : libmasa.cpp
• ARG_MASANET_CONNECT : libmasa.cpp
• ARG_MAX_ALIGNMENTS : libmasa.cpp
• ARG_MAXIMUM_PARTITION : libmasa.cpp
• ARG_NO_BLOCK_PRUNING : libmasa.cpp
• ARG_NO_FLUSH : libmasa.cpp
• ARG_NOT_ORTHOGONAL : libmasa.cpp
• ARG_OUTPUT_FORMAT : libmasa.cpp
• ARG_PART : libmasa.cpp
• ARG_PREDICTED_TRACEBACK : libmasa.cpp
• ARG_RAM_SIZE : libmasa.cpp
• ARG_REVERSE : libmasa.cpp
• ARG_REVERSE_COMPLEMENT : libmasa.cpp
• ARG_SHARED_DIR : libmasa.cpp
• ARG_SPECIAL_ROWS_DIR : libmasa.cpp
• ARG_SPLIT : libmasa.cpp
• ARG_STAGE_1 : libmasa.cpp
• ARG_STAGE_2 : libmasa.cpp
• ARG_STAGE_3 : libmasa.cpp
• ARG_STAGE_4 : libmasa.cpp
• ARG_STAGE_5 : libmasa.cpp
• ARG_STAGE_6 : libmasa.cpp
• ARG_TEST : libmasa.cpp
• ARG_TRIM : libmasa.cpp
• ARG_VERBOSE : libmasa.cpp
• ARG_WAIT_PART : libmasa.cpp
• ARG_WORK_DIR : libmasa.cpp
• ARGUMENT_ERROR : IAlignerParameter.hpp
• ARGUMENT_ERROR_NO_OPTION : IAlignerParameter.hpp
• ARGUMENT_ERROR_NOT_FOUND : IAlignerParameter.hpp
• ARGUMENT_OK : IAlignerParameter.hpp
• AT_ANYWHERE : Job.hpp
• AT_NOWHERE : Job.hpp
• AT_SEQUENCE_1 : Job.hpp
• AT_SEQUENCE_1_AND_2 : Job.hpp
• AT_SEQUENCE_1_OR_2 : Job.hpp
• AT_SEQUENCE_2 : Job.hpp
• AUTO_GRID_SIZE : BlockAlignerParameters.cpp