Global Namespace

// namespaces

namespace std
namespace xf
    namespace xf::genomics

// structs

struct FPGAInput
struct Hap
struct InputDataPackOpt
struct Read
struct hapLenPack
struct pairhmmInput
struct pairhmmOutput
struct readDataPack
struct readInfo
struct testcase

// unions

union ieee754
union ieee754s

// classes

template <class NUMBER>
class Context

template <>
class Context <double>

template <>
class Context <float>

template <class NUMBER>
class ContextBase

class ConvertChar
class xilPairHMM

// global variables

constexpr auto c_occ_intv_shift
constexpr auto c_occ_interval
constexpr auto c_occ_intv_mask
constexpr auto c_min_seed_len
constexpr auto c_split_width
constexpr auto c_split_len
constexpr auto c_max_mem_intv
constexpr auto c_max_intv_alloc
constexpr auto c_seq_length
constexpr auto c_max_batch_size
constexpr auto c_max_tile_size
constexpr auto c_batch_size
const char bases[5]
double avg_numReads
double avg_numHaps
int case_counter
uint64_t exceptions_array[128]
FILE* g_debug_fptr

// macros

#define ABSMAXCOST
#define AMBIG_CHAR
#define AVX_PERF
#define BPSZ

#define CAT( \
    X, \
    Y \
    )

#define CONCAT( \
    X, \
    Y \
    )

#define CONVERT_AND_PRINT(X)
#define DEP_DIST
#define DIE_NUM
#define END_OFFSET
#define FPGA_PERF
#define GAP
#define GMEM_DWIDTH
#define GMEM_DWIDTH
#define GapM
#define HAP_BLOCK_SIZE
#define HAP_DATA_OFFSET
#define HAP_LEN_OFFSET
#define ITERNUM_OFFSET
#define JACOBIAN_LOG_TABLE_INV_STEP
#define JACOBIAN_LOG_TABLE_INV_STEP
#define JACOBIAN_LOG_TABLE_INV_STEP
#define JACOBIAN_LOG_TABLE_SIZE
#define JACOBIAN_LOG_TABLE_SIZE
#define JACOBIAN_LOG_TABLE_STEP
#define JACOBIAN_LOG_TABLE_STEP
#define JACOBIAN_LOG_TABLE_STEP
#define KERNEL_NUM
#define LN10_HEX
#define LOG10_CACHE_SIZE
#define M2M_INIT
#define MATCH
#define MAXCOL
#define MAXN
#define MAXPE
#define MAXROW
#define MAX_HAPDATA_NUM
#define MAX_HAP_LEN
#define MAX_JACOBIAN_TOLERANCE
#define MAX_JACOBIAN_TOLERANCE
#define MAX_JACOBIAN_TOLERANCE
#define MAX_QUAL
#define MAX_QUAL
#define MAX_QUAL
#define MAX_READ_LEN
#define MAX_RSDATA_NUM
#define MINVAL
#define MIN_ACCEPTED
#define MISS_MATCH
#define MM
#define MX
#define MY
#define NUMITER
#define NUMPACKED
#define NUMREADPU_OFFSET
#define NUM_BLOCKS
#define NUM_DISTINCT_CHARS
#define PACKEDSZ
#define PACKEDSZ_K
#define PH2PR_10
#define PH2PR_DIV3_INIT
#define PH2PR_INIT
#define PH2PR_SUB1_10
#define PH2PR_SUB1_INIT

#define READREFUINTSZ( \
    X, \
    Y \
    )

#define READ_BLOCK_SIZE
#define READ_DATA_OFFSET
#define READ_INFO_OFFSET

#define SET_MATCH_TO_MATCH_PROB( \
    output, \
    insQual, \
    delQual \
    )

#define SLR0_PE_NUM
#define SLR1_PE_NUM
#define SLR2_PE_NUM

#define STORE_FP_EXCEPTIONS( \
    flagp, \
    exceptions_array \
    )

#define TOTAL_PE_NUM
#define TRANSITION_deletionToDeletion
#define TRANSITION_indelToMatch
#define TRANSITION_insertionToInsertion
#define TRANSITION_matchToDeletion
#define TRANSITION_matchToInsertion
#define TRANSITION_matchToMatch
#define TRANS_PROB_ARRAY_LENGTH
#define UINTNUMBP
#define UINTNUMBP_K
#define UINTSZ
#define UINTSZ_K
#define XX
#define YY
#define _SMEMMODULES_HPP
#define __constant
#define __global
#define __kernel