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/seqalign/trunk/sw_gen_testbench.v
0,0 → 1,160
module sw_gen_testbench;
/*(clk,
rst,
i_targ_length,
target,
i_vld,
i_data,
o_vld,
m_result
);*/
 
localparam
SCORE_WIDTH = 11,
N_A = 2'b00, //nucleotide "A"
N_G = 2'b01, //nucleotide "G"
N_T = 2'b10, //nucleotide "T"
N_C = 2'b11, //nucleotide "C"
INS = 1, //insertion penalty
DEL = 1, //deletion penalty
TB_UP = 2'b00, //"UP" traceback pointer
TB_DIAG = 2'b01, //"DIAG" traceback pointer
TB_LEFT = 2'b10; //"LEFT" traceback pointer
 
parameter LOGLENGTH=3; //log2(total number of comparison blocks instantiated)
parameter LENGTH = 4; //total number of comparison blocks instantiated - target length must be less than this
 
reg rst;
reg clk;
reg i_local;
reg [1:0] i_data;
 
wire [LOGLENGTH-1:0] i_targ_length; //this is the (length_of_the_actual_target_string - 1) (must be less than the max length value - 0=1 block, 1=2 blocks, etc)
wire [(LENGTH*2-1):0] target; //this is the actual target sequence - target[1:0] goes into block0, target[3:2] goes into block1, etc.
 
wire o_vld;
wire [SCORE_WIDTH-1:0] m_result;
wire [SCORE_WIDTH-1:0] i_result;
wire [SCORE_WIDTH-1:0] h_result;
wire [2*(LENGTH-1)+1:0] data;
 
reg i_vld; //master valid signal at start of chain
wire vld[LENGTH-1:0];
wire reset[LENGTH-1:0];
 
//wire [SCORE_WIDTH*(LENGTH-1)+SCORE_WIDTH-1:0] right;
wire [SCORE_WIDTH-1:0] right_m [LENGTH-1:0];
wire [SCORE_WIDTH-1:0] right_i [LENGTH-1:0];
wire [SCORE_WIDTH-1:0] high [LENGTH-1:0];
wire [LENGTH-1:0] gap;
 
//wire [LENGTH-1:0] done;
 
reg [SCORE_WIDTH-1:0] final_score;
 
 
 
assign o_vld = vld[3];
//assign m_result = right[i_targ_length];
 
assign target={N_G,N_C,N_C,N_C};
//assign i_targ_length = 3;
genvar i;
 
assign i_targ_length = 2'b11;
assign m_result = right_m[LENGTH-1];
assign i_result = right_i[LENGTH-1];
assign h_result = high[LENGTH-1];
 
generate
for (i=0; i < LENGTH; i = i + 1)
begin: pe_block
if (i == 0) //first module in auto-generated chain
sw_pe_affine #(.LENGTH(LENGTH), .LOGLENGTH(LOGLENGTH))
pe0 (.clk(clk),
.i_rst(rst),
.o_rst(reset[i]),
.i_data(i_data[1:0]),
.i_preload(target[1:0]),
.i_left_m(11'b10000000000),
.i_left_i(11'b10000000000),
.i_lgap(1'b0),
.i_vld(i_vld),
.i_local(i_local),
.o_right_m(right_m[i]),
.o_right_i(right_i[i]),
.i_high(11'b10000000000),
.o_high(high[i]),
.o_rgap(gap[i]),
.o_vld(vld[i]),
.o_data(data[2*i+1:2*i]),
.start(1'b1));
//.done(done[i]));
else //modules other than first one
sw_pe_affine #(.LENGTH(LENGTH), .LOGLENGTH(LOGLENGTH))
pe1 (.clk(clk),
.i_rst(reset[i-1]),
.o_rst(reset[i]),
.i_data(data[2*(i-1)+1:(i-1)*2]),
.i_preload(target[i*2+1:i*2]),
.i_left_m(right_m[i-1]),
.i_left_i(right_i[i-1]),
.i_lgap(gap[i-1]),
.i_vld(vld[i-1]),
.i_local(i_local),
.o_right_m(right_m[i]),
.o_right_i(right_i[i]),
.i_high(high[i-1]),
.o_high(high[i]),
.o_rgap(gap[i]),
.o_vld(vld[i]),
.o_data(data[2*(i)+1:2*(i)]),
.start(1'b0));
// .done(done[i]));
 
end
 
endgenerate
 
 
 
 
initial
begin
$dumpfile("sw_gen_testbench.dump");
$dumpvars (0,sw_gen_testbench);
rst <= 1'b1;
clk <= 1'b0;
i_vld <= 1'b0;
i_data <= 2'b00;
i_local <= 1'b1;
#22
rst <= 1'b0;
#100
i_data <= N_G;
i_vld <= 1'b1;
#20
i_data <= N_G;
#20
i_data <= N_G;
#20
i_data <= N_C;
#20
i_vld <= 1'b0;
#200
$finish();
 
end
 
always
begin
#10 clk <= ~clk;
end
 
 
 
 
 
 
 
endmodule
/seqalign/trunk/sw_pe_affine.v
0,0 → 1,178
module sw_pe_affine(clk,
i_rst,
o_rst,
i_data,
i_preload,
i_left_m,
i_left_i,
i_high,
i_vld,
i_local,
o_right_m,
o_right_i,
o_high,
o_vld,
o_data,
start);
 
localparam
SCORE_WIDTH = 11,
N_A = 2'b00, //nucleotide "A"
N_G = 2'b01, //nucleotide "G"
N_T = 2'b10, //nucleotide "T"
N_C = 2'b11, //nucleotide "C"
INS_START = 3, //insertion penalty
INS_CONT = 1,
DEL_START = 3, //deletion penalty
DEL_CONT = 1,
TB_UP = 2'b00, //"UP" traceback pointer
TB_DIAG = 2'b01, //"DIAG" traceback pointer
TB_LEFT = 2'b10, //"LEFT" traceback pointer
GOPEN = 12,
GEXT = 4;
 
input wire clk;
input wire i_rst;
output reg o_rst;
input wire [1:0] i_data; //sequence being streamed in
input wire [1:0] i_preload; //fixed character assigned to this node
input wire [SCORE_WIDTH-1:0] i_left_m; //connection to left neighbor cell for M matrix
input wire [SCORE_WIDTH-1:0] i_left_i; //connection to left neighbor cell for I matrix
input wire i_vld; //valid data coming from neighbor
input wire i_local; //=1 if local alignment, =0 if global alignment
input wire start; //designate that you're on the left edge of the array
input wire [SCORE_WIDTH-1:0] i_high; //input of highest score from neighbor
output reg [SCORE_WIDTH-1:0] o_right_m; //output of score from t-1 for M matrix
output reg [SCORE_WIDTH-1:0] o_right_i; //output of score for t-1 for I matrix
output reg [SCORE_WIDTH-1:0] o_high; //output of currently highest score
 
output reg o_vld; //tells neighbor data is valid
output reg [1:0] o_data;
 
 
 
parameter LENGTH=48;
parameter LOGLENGTH = 6;
 
reg [1:0] state; //just state counter
 
reg [SCORE_WIDTH-1:0] l_diag_score_m;
reg [SCORE_WIDTH-1:0] l_diag_score_i;
 
wire [SCORE_WIDTH-1:0] right_m_nxt;
wire [SCORE_WIDTH-1:0] right_i_nxt;
wire [SCORE_WIDTH-1:0] left_open;
wire [SCORE_WIDTH-1:0] left_ext;
wire [SCORE_WIDTH-1:0] up_open;
wire [SCORE_WIDTH-1:0] up_ext;
wire [SCORE_WIDTH-1:0] left_max;
wire [SCORE_WIDTH-1:0] up_max;
wire [SCORE_WIDTH-1:0] rightmax;
wire [SCORE_WIDTH-1:0] start_left;
 
reg [SCORE_WIDTH-1:0] match;
wire [SCORE_WIDTH-1:0] max_score_a;
wire [SCORE_WIDTH-1:0] max_score_b;
wire [SCORE_WIDTH-1:0] left_score;
wire [SCORE_WIDTH-1:0] up_score;
wire [SCORE_WIDTH-1:0] diag_score;
wire [SCORE_WIDTH-1:0] neutral_score;
 
wire [SCORE_WIDTH-1:0] left_score_b;
 
 
//compute new score options
 
assign neutral_score = 11'b10000000000;
 
assign start_left = (state==2'b01) ? (l_diag_score_m - GOPEN) : (l_diag_score_m - GEXT);
 
assign left_open = i_left_m - GOPEN;
assign left_ext = i_left_i - GEXT;
assign up_open = o_right_m - GOPEN;
assign up_ext = o_right_i - GEXT;
assign left_max = start ? start_left : ((left_open > left_ext) ? left_open : left_ext);
assign up_max = (up_open > up_ext) ? up_open : up_ext;
 
assign right_m_nxt = match + ((l_diag_score_m > l_diag_score_i) ? l_diag_score_m : l_diag_score_i); //next m score
assign right_i_nxt = (left_max > up_max) ? left_max : up_max;
 
 
 
always@(posedge clk)
o_rst <= i_rst;
always@*
case({i_data[1:0],i_preload[1:0]})
//this is the match-score lookup table: +5 for a match, -4 for a mismatch
{N_A,N_A}:match = 11'b101; //+5
{N_A,N_G}:match = 11'h7fc; //-4
{N_A,N_T}:match = 11'h7fc;
{N_A,N_C}:match = 11'h7fc;
{N_G,N_A}:match = 11'h7fc;
{N_G,N_G}:match = 11'b101;
{N_G,N_T}:match = 11'h7fc;
{N_G,N_C}:match = 11'h7fc;
{N_T,N_A}:match = 11'h7fc;
{N_T,N_G}:match = 11'h7fc;
{N_T,N_T}:match = 11'b101;
{N_T,N_C}:match = 11'h7fc;
{N_C,N_A}:match = 11'h7fc;
{N_C,N_G}:match = 11'h7fc;
{N_C,N_T}:match = 11'h7fc;
{N_C,N_C}:match = 11'b101;
endcase
 
//just propagate the valid signal
always@(posedge clk)
if (i_rst==1'b1)
o_vld <= 1'b0;
else
o_vld <= i_vld;
 
 
//This continuously calculates the highest score to pass through the block
assign rightmax = (right_m_nxt > right_i_nxt) ? right_m_nxt : right_i_nxt;
 
 
always@(posedge clk)
begin
if (i_rst==1'b1)
o_high <= neutral_score; //reset to "0"
else if (i_vld==1'b1)
o_high <= (o_high > rightmax) ? ( (o_high > i_high) ? o_high : i_high) : ((rightmax > i_high) ? rightmax : i_high);
end
 
 
always@(posedge clk) begin
if (i_rst==1'b1) begin
//This is where we initialize the matrix
o_right_m <= i_local ? neutral_score : (i_left_m - (start ? GOPEN : GEXT)); //init m matrix
o_right_i <= i_local ? neutral_score : (i_left_i - (start ? GOPEN : GEXT)); //init i matrix
o_data[1:0] <= 2'b00;
l_diag_score_m <= start ? neutral_score : (i_local ? neutral_score : i_left_m);
l_diag_score_i <= start ? neutral_score : (i_local ? neutral_score : i_left_i);
end
else if (i_vld==1'b1) begin
o_data[1:0] <= i_data[1:0];
o_right_m <= (i_local ? ((right_m_nxt > neutral_score) ? right_m_nxt : neutral_score) : right_m_nxt);
o_right_i <= (i_local ? ((right_i_nxt > neutral_score) ? right_i_nxt : neutral_score) : right_i_nxt);
l_diag_score_m <= start ? (i_local ? neutral_score : (l_diag_score_m - GEXT)) : i_left_m ;
l_diag_score_i <= start ? (i_local ? neutral_score : (l_diag_score_i - GEXT)) : i_left_i ;
end
end
 
always@(posedge clk) begin
if (i_rst)
state <= 2'b00;
else begin
case(state[1:0])
2'b00:state[1:0] <= 2'b01; //reset state
2'b01:if (i_vld==1'b1) state[1:0] <= 2'b10; //INIT state
2'b10:if (i_vld==1'b0) state[1:0] <= 2'b01; //SCORE state - i_vld must be held high from the start of the query sequence to the end of it
2'b11:if (i_rst) state[1:0] <= 2'b00; //END state
endcase
end
end
endmodule
seqalign/trunk/sw_pe_affine.v Property changes : Added: svn:executable ## -0,0 +1 ## +* \ No newline at end of property Index: seqalign/trunk/README.txt =================================================================== --- seqalign/trunk/README.txt (nonexistent) +++ seqalign/trunk/README.txt (revision 2) @@ -0,0 +1,26 @@ +This is the initial release of the code. + +sw_pe_affine.v is the module of the 'processing elements' that +make up the systolic array. + +sw_gen_affine.v is the 'top level' file that instantiates an +array of PEs. It is fairly easily configurable to make the array +shorter or longer (by modifying the LENGTH and LOGLENGTH local params). + +sw_gen_testbench.v is a small testbench which instantiates a 4-PE +array and compares two 4 x 4 DNA sequences. + +sw_gen_affine should be instantiated by the toplevel block of your design, +along with the custom interface glue necessary to connect them. + +To operate the block, a query value (a packed array containing encoded 2-bit +nucleotides) and length (in nucleotides) should be set as inputs. Then, a reset +pulse should be sent down the array. Then, the i_vld (valid) signal should be +held high as the comparison string is clocked in, two bits at a time, until +the string is completed and the i_vld signal is lowered. When the o_vld signal +goes low, the array is done processing and the result is ready. If the "local" +bit is high, the result will be on the "o_high" output of the last element. If +the "local" bit is low (global alignment mode), the valid result will be the +higher of the two "o_right_*" outputs of the last element. + +Happy Sequencing! Index: seqalign/trunk/sw_gen_affine.v =================================================================== --- seqalign/trunk/sw_gen_affine.v (nonexistent) +++ seqalign/trunk/sw_gen_affine.v (revision 2) @@ -0,0 +1,101 @@ +module sw_gen_affine(clk, + rst, + i_query_length, + i_local, + query, + i_vld, + i_data, + o_vld, + m_result + ); + +localparam + SCORE_WIDTH = 11, + N_A = 2'b00, //nucleotide "A" + N_G = 2'b01, //nucleotide "G" + N_T = 2'b10, //nucleotide "T" + N_C = 2'b11, //nucleotide "C" + INS = 1, //insertion penalty + DEL = 1, //deletion penalty + TB_UP = 2'b00, //"UP" traceback pointer + TB_DIAG = 2'b01, //"DIAG" traceback pointer + TB_LEFT = 2'b10; //"LEFT" traceback pointer + +parameter LOGLENGTH=6; //log2(total number of comparison blocks instantiated) +//parameter LENGTH = 1 << LOGLENGTH; //total number of comparison blocks instantiated - query length must be less than this +parameter LENGTH = 48; + +input wire rst; +input wire clk; +input wire [1:0] i_data; +input wire i_local; //=1 if local alignment, =0 if global alignment +input wire [LOGLENGTH-1:0] i_query_length; //this is the (length_of_the_actual_query_string - 1) (must be less than the max length value - 0=1 block, 1=2 blocks, etc) +input wire [(LENGTH*2-1):0] query; //this is the actual query sequence - query[1:0] goes into block0, query [3:2] goes into block1, etc. + +output wire o_vld; +output wire [SCORE_WIDTH-1:0] m_result; + +wire [2*(LENGTH-1)+1:0] data; + +input wire i_vld; //master valid signal at start of chain +wire vld[LENGTH-1:0]; + +wire [SCORE_WIDTH-1:0] right_m[LENGTH-1:0]; //the 'match' matrix cell value array +wire [SCORE_WIDTH-1:0] right_i[LENGTH-1:0]; //the 'indel' matrix cell value array +wire [SCORE_WIDTH-1:0] high_score [LENGTH-1:0]; //the 'current highest score' array +wire [LENGTH-1:0] gap; +wire [LENGTH-1:0] reset; + + +assign o_vld = vld[i_query_length]; +assign m_result = i_local ? high_score[i_query_length] : ((right_m[i_query_length] > right_i[i_query_length]) ? right_m[i_query_length] : right_i[i_query_length]); + +//assign query={N_A,N_G,N_T,N_T}; + +genvar i; +generate +for (i=0; i < LENGTH; i = i + 1) + begin: pe_block + if (i == 0) //first processing element in auto-generated chain + begin: pe_block0 + sw_pe_affine pe0(.clk(clk), + .i_rst(rst), + .o_rst(reset[i]), + .i_data(i_data[1:0]), + .i_preload(query[1:0]), + .i_left_m(11'b10000000000), + .i_left_i(11'b10000000000), + .i_vld(i_vld), + .i_local(i_local), + .i_high(11'b0), + .o_right_m(right_m[i]), + .o_right_i(right_i[i]), + .o_high(high_score[i]), + .o_vld(vld[i]), + .o_data(data[2*i+1:2*i]), + .start(1'b1)); + end + else //processing elements other than first one + begin: pe_block1 + sw_pe_affine pe1(.clk(clk), + .i_rst(reset[i-1]), + .o_rst(reset[i]), + .i_data(data[2*(i-1)+1:(i-1)*2]), + .i_preload(query[i*2+1:i*2]), + .i_left_m(right_m[i-1]), + .i_left_i(right_i[i-1]), + .i_local(i_local), + .i_vld(vld[i-1]), + .i_high(high_score[i-1]), + .o_right_m(right_m[i]), + .o_right_i(right_i[i]), + .o_high(high_score[i]), + .o_vld(vld[i]), + .o_data(data[2*(i)+1:2*(i)]), + .start(1'b0)); + end + end +endgenerate + + +endmodule \ No newline at end of file
seqalign/trunk/sw_gen_affine.v Property changes : Added: svn:executable ## -0,0 +1 ## +* \ No newline at end of property

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