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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,136 @@ | ||
| #include <stdlib.h> | ||
| #include <stdint.h> | ||
| #include <assert.h> | ||
| #include <emmintrin.h> | ||
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| #include <iostream> | ||
| #include <verilated.h> // Defines common routines | ||
| #include "Vscore_matrix_compute.h" // From Verilating "bin2bcd.v" | ||
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| #define C_NULL 5 | ||
| #define C_FILL 6 // filler string to drain buffer | ||
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| #ifdef __cplusplus | ||
| extern "C" { | ||
| #endif | ||
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| int sequence_counter = 0; | ||
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| int ksw_extend_hw(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off) | ||
| { | ||
| Vscore_matrix_compute *top = new Vscore_matrix_compute(); // Create local instance for multi threading | ||
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| const uint8_t *query_itr, *target_itr; | ||
| int score = 0; | ||
| int row_score = 0; | ||
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| unsigned int main_time = 0; // Current simulation time | ||
| bool computing = false; | ||
| bool compute_done = false; | ||
| int min_seq_len = (int)(sizeof(top->score_matrix_compute__DOT__h_row1) * 2) ; // BW*2 to drain... | ||
| int num_chars_sent = 0; | ||
| bool zero_row_exists = false, row_score_released = false; | ||
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| top->rst = 1; // Set some inputs | ||
| top->clk = 0; | ||
| top->start_i = 0; | ||
| top->init_score_i = h0; | ||
| top->query_entry_i = C_NULL; | ||
| top->target_entry_i = C_NULL; | ||
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| while (!Verilated::gotFinish()) { | ||
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| if ((main_time % 5) == 0) | ||
| top->clk = !top->clk; // Toggle clock | ||
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| if (main_time > 10) { // Release reset | ||
| top->rst = 0; | ||
| } | ||
| // Assert start flag | ||
| if (main_time > 21 && !computing && top->start_i == 0) { | ||
| top->start_i = 1; | ||
| // printf("#%d setting start_i\n", main_time); | ||
| } | ||
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| // Query sequence | ||
| if ((main_time % 10) == 1 && (top->start_i == 1 || computing)) { | ||
| if (!computing) { | ||
| // printf("#%d sequencing start\n", main_time); | ||
| top->start_i = 0; | ||
| computing = true; | ||
| query_itr = query; | ||
| target_itr = target; | ||
| } | ||
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| top->query_entry_i = C_NULL; | ||
| top->target_entry_i = C_NULL; | ||
| if (query_itr - query < qlen || target_itr - target < tlen) { | ||
| top->query_entry_i = C_FILL; | ||
| top->target_entry_i = C_FILL; | ||
| if (query_itr - query < qlen) { | ||
| top->query_entry_i = *query_itr; | ||
| query_itr++; | ||
| } | ||
| if (target_itr - target < tlen) { | ||
| top->target_entry_i = *target_itr; | ||
| target_itr++; | ||
| } | ||
| num_chars_sent++; | ||
| // printf("#%d sequencing char (%c,%c) at %d\n", main_time, "ACGTN"[(int)*(query_itr-1)], "ACGTN"[(int)*(target_itr-1)], query_itr - query); | ||
| } else if (num_chars_sent < min_seq_len) { | ||
| top->query_entry_i = C_FILL; | ||
| top->target_entry_i = C_FILL; | ||
| num_chars_sent++; | ||
| } | ||
| } | ||
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| top->eval(); // Evaluate model | ||
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| // Monitor score output | ||
| if ((main_time % 10) == 1 && computing && top->max_row_score_o >= 0 && !zero_row_exists) { | ||
| // row_score = row_score < top->max_score_o? top->max_score_o: row_score; | ||
| row_score = row_score < top->max_row_score_o? top->max_row_score_o: row_score; | ||
| if (top->max_row_score_o > 0 && ! row_score_released) { | ||
| row_score_released = true; | ||
| } else if (top->max_row_score_o == 0 && row_score_released) { | ||
| zero_row_exists = true; | ||
| score = row_score < h0 ? h0 : row_score; | ||
| } | ||
| } | ||
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| // Wait for done | ||
| if ((main_time % 10) == 1 && computing && top->done_o) { | ||
| compute_done = true; | ||
| } | ||
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| // Read the output | ||
| else if ((main_time % 10) == 1 && compute_done) { | ||
| // score = top->max_score_o; | ||
| score = !score? row_score : score; | ||
| // printf("#%d\t SEQ %d\t initial_score %d\t computed_score %d\n", main_time, sequence_counter, h0, top->max_score_o); | ||
| computing = false; | ||
| compute_done = false; | ||
| num_chars_sent = 0; | ||
| zero_row_exists = false; | ||
| row_score_released = false; | ||
| sequence_counter++; | ||
| // printf("@@@ Done processing\n"); | ||
| break; | ||
| } | ||
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| main_time++; // Time passes... | ||
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| } | ||
| // Read the output | ||
| top->final(); | ||
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| delete top; | ||
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| return score; | ||
| } | ||
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| #ifdef __cplusplus | ||
| } | ||
| #endif |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,8 @@ | ||
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| #ifndef __AC_KSW_W_H | ||
| #define __AC_KSW_W_H | ||
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| #include <stdint.h> | ||
| int ksw_extend_hw(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off); | ||
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| #endif |