Global Namespace

// typedefs

typedef ap_uint <4> uint4_t
typedef ap_uint <512> uint512_t

// macros

#define BATCH_SIZE
#define MAX_INTV
#define MAX_INTV_ALLOC
#define SEQ_LENGTH

Global Functions

opencl_sw_maxscore

#include "opencl_sw_maxscore_systolic.hpp"

void opencl_sw_maxscore (
    ap_uint <NUMPACKED*2>* input,
    ap_uint <NUMPACKED*2>* output,
    int* size
    )

Systolic implementation of smith-waterman.

Parameters:

input	input raw data
output	max score
size	number of iterations

pairhmm

#include "pairhmm.hpp"

void pairhmm (
    ap_uint <GMEM_DWIDTH>* in,
    float* output_data,
    int numRead,
    int numHap
    )

PairHMM kernel takes read/ref sequence as input and generates the likelihood ratio.

Parameters:

in	input sequence data
output_data	likelihood ratio
numRead	number of read sequences
numHap	number of hap sequences

mem_collect_intv_core

#include "smem.hpp"

void mem_collect_intv_core (
    ap_uint <512>* bwt,
    ap_uint <256>* mem,
    ap_uint <64>* bwt_para,
    ap_uint <32>* mem_num,
    uint8_t* seq,
    uint8_t* seq_len,
    int batch_size
    )

SMEM kernel takes the input sequence and BWT tranformation and generates super maximal exact match.

Parameters:

bwt	bwt sequence
mem	output
bwt_para	bwt parameters
mem_num	number of output maximal matches
seq	input sequence
seq_len	sequence length
batch_size	batch size