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kernels3.cu
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kernels3.cu
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#include <curand_kernel.h>
extern "C"
{
texture<unsigned char, 2> tex;
// texture<float, 2, cudaReadModeElementType> texData;
typedef struct frag {
int* pos;
int* id_c;
int* start_bp;
int* len_bp;
int* circ;
int* id;
int* prev;
int* next;
int* l_cont;
int* l_cont_bp;
int* ori;
int* rep;
int* activ;
int* id_d;
} frag;
typedef struct __attribute__ ((packed)) param_simu {
float kuhn __attribute__ ((packed));
float lm __attribute__ ((packed));
float c1 __attribute__ ((packed));
float slope __attribute__ ((packed));
float d __attribute__ ((packed));
float d_max __attribute__ ((packed));
float fact __attribute__ ((packed));
float v_inter __attribute__ ((packed));
} param_simu;
#if !defined(__CUDA_ARCH__) || __CUDA_ARCH__ >= 600
#else
__device__ double atomicAdd(double* address, double val)
{
unsigned long long int* address_as_ull = (unsigned long long int*)address;
unsigned long long int old = *address_as_ull, assumed;
do {
assumed = old;
old = atomicCAS(address_as_ull, assumed,
__double_as_longlong(val +
__longlong_as_double(assumed)));
} while (assumed != old);
return __longlong_as_double(old);
}
#endif
__global__ void init_rng(int nthreads, curandState *s, unsigned long long seed, unsigned long long offset)
{
int id = blockIdx.x*blockDim.x + threadIdx.x;
if (id >= nthreads)
return;
curand_init(seed, id, offset, &s[id]);
}
__global__ void gen_rand_mat(float* initArray, float *randArray, curandState *state, int n_rng, int width,
float fact_sub)
{
int r0 = threadIdx.x + blockDim.x * blockIdx.x;
int r1 = threadIdx.y + blockDim.y * blockIdx.y;
int coord = r0 * width + r1;
int coord_y = r1 * width + r0;
int id_rng = coord % n_rng ;
float val;
if ((r0<width) && (r1 < r0)) {
float mean_exp = initArray[coord] * fact_sub;
float mean = max(mean_exp, 0.000001);
val = curand_poisson(&state[id_rng], mean);
randArray[coord] = val;
randArray[coord_y] = val;
}
}
__device__ float factorial(float n)
{
float result = 1;
n = floor(n);
if (n<10){
for(int c = 1 ; c <= n ; c++ )
result = result * c;
}
else{
result = powf(n,n) * exp(-n) * sqrtf(2 * M_PI * n);
}
return ( result );
}
__device__ param_simu modify_param_simu(int id_modifier, param_simu p, float var)
{
param_simu out;
if (id_modifier == 0){
out.kuhn = p.kuhn;
out.lm = p.lm;
out.slope = p.slope;
out.d = var;
out.c1 = p.c1;
out.d_max = p.d_max;
out.v_inter = p.v_inter;
out.fact = p.fact;
}
else if (id_modifier == 1){
out.kuhn = p.kuhn;
out.lm = p.lm;
out.slope = var;
out.d = p.d;
out.c1 = p.c1;
out.d_max = p.d_max;
out.v_inter = p.v_inter;
out.fact = p.fact;
}
return (out);
}
__device__ float rippe_contacts(float s, param_simu p)
{
// s = distance in kb
// p = model's parameters
float result = 0.0f;
if ((s>0.0f) && (s<p.d_max)){
result = (p.c1 * pow(s, p.slope) * exp((p.d-2)/(pow(s*p.lm/p.kuhn, 2.0f ) + p.d) )) * p.fact;
}
float out = max(result, p.v_inter);
// else{
// result = p.v_inter;
// }
return ( out );
}
__device__ float rippe_contacts_circ(float s, float s_tot, param_simu p)
{
// s = distance in kb
// p = model's parameters
// s_tot = total length of circular contig
float result = 0.0f;
float n_dist = 1.0f;
float n_tot = 1.0f;
float n = 1.0f;
float K = 1.0f;
float norm_circ, norm_lin, nmax, val;
if ((s > 0.0f) && (s < p.d_max)){
// if ((s < s_tot) && (s > 0.0) && (s < p.d_max)){
K = p.lm / p.kuhn;
n_dist = s ;
n_tot = s_tot;
nmax = K * 1;
n = K * n_dist *(n_tot - n_dist) / n_tot;
norm_lin = rippe_contacts(s, p);
norm_circ = (powf(p.kuhn, -3.0f) * powf(nmax, p.slope) * expf((p.d - 2.0f)/(powf(nmax, 2.0f ) + p.d))) * p.fact;
val = (powf(p.kuhn, -3.0f) * powf(n, p.slope) * expf((p.d - 2.0f)/(powf(n, 2.0f ) + p.d))) * p.fact;
result = val * norm_lin / norm_circ;
}
float out = max(result, p.v_inter);
// else{
// result = p.v_inter;
// }
return ( out );
}
__device__ float evaluate_likelihood_float(float ex, float ob)
{
// ex = expected n contacts
// ob = observed n contacts
float res = 0;
float lim = 15;
if (ex != 0){
if (ob >=lim){
res = ob * logf(ex) - ex - (ob * logf(ob) - ob + logf(sqrtf(ob * 2.0f * M_PI)));
}
else if ((ob>0) && (ob<lim)){
res = ob * logf(ex) - ex - logf(factorial(ob));
}
else if (ob==0){
res = - ex;
}
}
return (res);
}
__device__ double evaluate_likelihood_double(double ex, double ob)
{
// ex = expected n contacts
// ob = observed n contacts
double res = 0;
double lim = 15;
if (ex != 0){
if (ob >=lim){
res = ob * log(ex) - ex - (ob * log(ob) - ob + log(sqrt(ob * 2.0 * M_PI)));
}
else if ((ob>0) && (ob<lim)){
res = ob * log(ex) - ex - log((double) factorial((float) ob));
}
else if (ob==0){
res = - ex;
}
}
return (res);
}
__device__ int2 lin_2_2dpos(int ind)
{
int i = ind + 1;
int x = (-0.5 + 0.5 * sqrt((float) 1 + 8 * (i - 1))) + 2;
int y = x * (3 - x) / 2 + i - 1;
//int2 out = (int2) (x - 1,y - 1);
int2 out;
out.x = min(x - 1, y -1);
out.y = max(x - 1, y - 1);
return (out);
}
__device__ int conv_plan_pos_2_lin(int2 pos)
{
int x = pos.x + 1;
int y = pos.y + 1;
int i = min(x,y);
int j = max(x,y);
int ind = (j * (j - 3)) / 2 + i;
// int ind = (j * (j - 3) / 2 + i + 1) - 1;
return ind;
}
__global__ void flip_frag(frag* fragArray,frag* o_fragArray, int id_f_flip,
int n_frags)
{
int id_frag = threadIdx.x + blockDim.x * blockIdx.x;
if (id_frag < n_frags){
int contig_fi = o_fragArray->id_c[id_frag];
int pos_fi = o_fragArray->pos[id_frag];
int l_cont_fi = o_fragArray->l_cont[id_frag];
int l_cont_bp_fi = o_fragArray->l_cont_bp[id_frag];
int len_bp_fi = o_fragArray->len_bp[id_frag];
int circ_fi = o_fragArray->circ[id_frag];
int id_prev_fi = o_fragArray->prev[id_frag];
int id_next_fi = o_fragArray->next[id_frag];
int start_bp_fi = o_fragArray->start_bp[id_frag];
int or_fi = o_fragArray->ori[id_frag];
int rep_fi = o_fragArray->rep[id_frag];
int activ_fi = o_fragArray->activ[id_frag];
int id_d_fi = o_fragArray->id_d[id_frag];
fragArray->pos[id_frag] = pos_fi;
fragArray->id_c[id_frag] = contig_fi;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = circ_fi;
fragArray->id[id_frag] = id_frag;
if (id_frag == id_f_flip){
fragArray->ori[id_frag] = or_fi * -1;
}
else{
fragArray->ori[id_frag] = or_fi;
}
fragArray->prev[id_frag] = id_prev_fi;
fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_fi;
fragArray->l_cont_bp[id_frag] = l_cont_bp_fi;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
__global__ void swap_activity_frag(frag* fragArray,frag* o_fragArray, int id_f_unactiv, int max_id_contig,
int n_frags)
{
int id_frag = threadIdx.x + blockDim.x * blockIdx.x;
if (id_frag < n_frags){
int contig_fi = o_fragArray->id_c[id_frag];
int pos_fi = o_fragArray->pos[id_frag];
int l_cont_fi = o_fragArray->l_cont[id_frag];
int l_cont_bp_fi = o_fragArray->l_cont_bp[id_frag];
int len_bp_fi = o_fragArray->len_bp[id_frag];
int circ_fi = o_fragArray->circ[id_frag];
int id_prev_fi = o_fragArray->prev[id_frag];
int id_next_fi = o_fragArray->next[id_frag];
int start_bp_fi = o_fragArray->start_bp[id_frag];
int or_fi = o_fragArray->ori[id_frag];
int rep_fi = o_fragArray->rep[id_frag];
int activ_fi = o_fragArray->activ[id_frag];
int id_d_fi = o_fragArray->id_d[id_frag];
fragArray->pos[id_frag] = pos_fi;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = circ_fi;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
// if ((id_frag == id_f_unactiv) && (id_d_fi != id_frag)){
if ((id_frag == id_f_unactiv) && (rep_fi == 1)){
fragArray->activ[id_frag] = 0 * (activ_fi == 1) + 1 * (activ_fi == 0);
fragArray->id_c[id_frag] = contig_fi * (activ_fi == 1) + (max_id_contig + 1) * (activ_fi == 0);
// fragArray->id_c[id_frag] = contig_fi * (activ_fi == 1) + (max_id_contig + 1) * (activ_fi == 0);
}
else{
fragArray->activ[id_frag] = activ_fi;
fragArray->id_c[id_frag] = contig_fi;
}
fragArray->prev[id_frag] = id_prev_fi;
fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_fi;
fragArray->l_cont_bp[id_frag] = l_cont_bp_fi;
fragArray->rep[id_frag] = rep_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
__global__ void pop_out_frag(frag* fragArray,frag* o_fragArray, int* pop_id_contigs, int id_f_pop,
int max_id_contig, int n_frags)
{
__shared__ int contig_f_pop;
__shared__ int pos_f_pop;
__shared__ int l_cont_f_pop;
__shared__ int l_cont_bp_f_pop;
__shared__ int len_bp_f_pop;
__shared__ int start_bp_f_pop;
__shared__ int id_prev_f_pop;
__shared__ int id_next_f_pop;
__shared__ int or_f_pop;
__shared__ int circ_f_pop;
int id_frag = threadIdx.x + blockDim.x * blockIdx.x;
if (threadIdx.x == 0){
contig_f_pop = o_fragArray->id_c[id_f_pop];
pos_f_pop = o_fragArray->pos[id_f_pop];
l_cont_f_pop = o_fragArray->l_cont[id_f_pop];
l_cont_bp_f_pop = o_fragArray->l_cont_bp[id_f_pop];
len_bp_f_pop = o_fragArray->len_bp[id_f_pop];
start_bp_f_pop = o_fragArray->start_bp[id_f_pop];
id_prev_f_pop = o_fragArray->prev[id_f_pop];
id_next_f_pop = o_fragArray->next[id_f_pop];
or_f_pop = o_fragArray->ori[id_f_pop];
circ_f_pop = o_fragArray->circ[id_f_pop];
}
__syncthreads();
if (id_frag < n_frags){
int contig_fi = o_fragArray->id_c[id_frag];
int pos_fi = o_fragArray->pos[id_frag];
int l_cont_fi = o_fragArray->l_cont[id_frag];
int l_cont_bp_fi = o_fragArray->l_cont_bp[id_frag];
int len_bp_fi = o_fragArray->len_bp[id_frag];
int circ_fi = o_fragArray->circ[id_frag];
int id_prev_fi = o_fragArray->prev[id_frag];
int id_next_fi = o_fragArray->next[id_frag];
int start_bp_fi = o_fragArray->start_bp[id_frag];
int or_fi = o_fragArray->ori[id_frag];
int rep_fi = o_fragArray->rep[id_frag];
int id_d_fi = o_fragArray->id_d[id_frag];
int activ_fi = o_fragArray->activ[id_frag];
if (l_cont_f_pop > 2){
if ( contig_fi == contig_f_pop){
if (pos_fi < pos_f_pop){
fragArray->pos[id_frag] = pos_fi;
fragArray->id_c[id_frag] = contig_fi;
pop_id_contigs[id_frag] = contig_fi;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = circ_fi;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
// fragArray->prev[id_frag] = id_prev_fi;
if ((id_frag == id_next_f_pop) && (circ_f_pop == 1)){
fragArray->prev[id_frag] = id_prev_f_pop;
}
else{
fragArray->prev[id_frag] = id_prev_fi;
}
if (pos_fi == (pos_f_pop - 1)){
fragArray->next[id_frag] = id_next_f_pop;
}
else{
fragArray->next[id_frag] = id_next_fi;
}
fragArray->l_cont[id_frag] = l_cont_fi -1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_fi - len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi == pos_f_pop){
fragArray->pos[id_frag] = 0;
fragArray->id_c[id_frag] = max_id_contig + 1;
pop_id_contigs[id_frag] = max_id_contig + 1;
fragArray->start_bp[id_frag] = 0;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = 1;
fragArray->prev[id_frag] = -1;
fragArray->next[id_frag] = -1;
fragArray->l_cont[id_frag] = 1;
fragArray->l_cont_bp[id_frag] = len_bp_fi;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi > pos_f_pop){
fragArray->pos[id_frag] = pos_fi - 1;
fragArray->id_c[id_frag] = contig_fi;
pop_id_contigs[id_frag] = contig_fi;
fragArray->start_bp[id_frag] = start_bp_fi - len_bp_f_pop;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = circ_fi;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
if (pos_fi == (pos_f_pop + 1)){
fragArray->prev[id_frag] = id_prev_f_pop;
}
else{
fragArray->prev[id_frag] = id_prev_fi;
}
if ((id_frag == id_prev_f_pop) && (circ_f_pop == 1)){
fragArray->next[id_frag] = id_next_f_pop;
}
else{
fragArray->next[id_frag] = id_next_fi;
}
// fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_fi -1 ;
fragArray->l_cont_bp[id_frag] = l_cont_bp_fi - len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
else{
fragArray->pos[id_frag] = pos_fi;
fragArray->id_c[id_frag] = contig_fi;
pop_id_contigs[id_frag] = contig_fi;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = circ_fi;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = id_prev_fi;
fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_fi;
fragArray->l_cont_bp[id_frag] = l_cont_bp_fi;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
else if (l_cont_f_pop == 2){
if ( contig_fi == contig_f_pop){
if (pos_fi < pos_f_pop){
fragArray->pos[id_frag] = pos_fi;
fragArray->id_c[id_frag] = contig_fi;
pop_id_contigs[id_frag] = contig_fi;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = -1;
fragArray->next[id_frag] = -1;
fragArray->l_cont[id_frag] = l_cont_fi -1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_fi - len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi == pos_f_pop){
fragArray->pos[id_frag] = 0;
fragArray->id_c[id_frag] = max_id_contig + 1;
pop_id_contigs[id_frag] = max_id_contig + 1;
fragArray->start_bp[id_frag] = 0;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = 1;
fragArray->prev[id_frag] = -1;
fragArray->next[id_frag] = -1;
fragArray->l_cont[id_frag] = 1;
fragArray->l_cont_bp[id_frag] = len_bp_fi;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi > pos_f_pop){
fragArray->pos[id_frag] = pos_fi - 1;
fragArray->id_c[id_frag] = contig_fi;
pop_id_contigs[id_frag] = contig_fi;
fragArray->start_bp[id_frag] = start_bp_fi - len_bp_f_pop;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = -1;
fragArray->next[id_frag] = -1;
fragArray->l_cont[id_frag] = l_cont_fi -1 ;
fragArray->l_cont_bp[id_frag] = l_cont_bp_fi - len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
else{
fragArray->pos[id_frag] = pos_fi;
fragArray->id_c[id_frag] = contig_fi;
pop_id_contigs[id_frag] = contig_fi;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = circ_fi;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = id_prev_fi;
fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_fi;
fragArray->l_cont_bp[id_frag] = l_cont_bp_fi;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
else{
fragArray->pos[id_frag] = pos_fi;
fragArray->id_c[id_frag] = contig_fi;
pop_id_contigs[id_frag] = contig_fi;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = circ_fi;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = id_prev_fi;
fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_fi;
fragArray->l_cont_bp[id_frag] = l_cont_bp_fi;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
}
__global__ void pop_in_frag_1(frag* fragArray,frag* o_fragArray, int id_f_pop, int id_f_ins, int max_id_contig,
int ori_f_pop,
int n_frags)
// split insert @ left
{
__shared__ int contig_f_pop;
__shared__ int pos_f_pop;
__shared__ int l_cont_f_pop;
__shared__ int l_cont_bp_f_pop;
__shared__ int len_bp_f_pop;
__shared__ int start_bp_f_pop;
__shared__ int id_prev_f_pop;
__shared__ int id_next_f_pop;
__shared__ int activ_f_pop;
// __shared__ int or_f_pop;
__shared__ int contig_f_ins;
__shared__ int pos_f_ins;
__shared__ int l_cont_f_ins;
__shared__ int l_cont_bp_f_ins;
__shared__ int len_bp_f_ins;
__shared__ int start_bp_f_ins;
__shared__ int id_prev_f_ins;
__shared__ int id_next_f_ins;
__shared__ int circ_f_ins;
__shared__ int or_f_ins;
__shared__ int activ_f_ins;
int id_frag = threadIdx.x + blockDim.x * blockIdx.x;
if (threadIdx.x == 0){
contig_f_pop = o_fragArray->id_c[id_f_pop];
pos_f_pop = o_fragArray->pos[id_f_pop];
l_cont_f_pop = o_fragArray->l_cont[id_f_pop];
l_cont_bp_f_pop = o_fragArray->l_cont_bp[id_f_pop];
len_bp_f_pop = o_fragArray->len_bp[id_f_pop];
start_bp_f_pop = o_fragArray->start_bp[id_f_pop];
id_prev_f_pop = o_fragArray->prev[id_f_pop];
id_next_f_pop = o_fragArray->next[id_f_pop];
activ_f_pop = o_fragArray->activ[id_f_pop];
contig_f_ins = o_fragArray->id_c[id_f_ins];
pos_f_ins = o_fragArray->pos[id_f_ins];
l_cont_f_ins = o_fragArray->l_cont[id_f_ins];
l_cont_bp_f_ins = o_fragArray->l_cont_bp[id_f_ins];
len_bp_f_ins = o_fragArray->len_bp[id_f_ins];
start_bp_f_ins = o_fragArray->start_bp[id_f_ins];
id_prev_f_ins = o_fragArray->prev[id_f_ins];
id_next_f_ins = o_fragArray->next[id_f_ins];
circ_f_ins = o_fragArray->circ[id_f_ins];
or_f_ins = o_fragArray->ori[id_f_ins];
activ_f_ins = o_fragArray->activ[id_f_ins];
}
__syncthreads();
if ((activ_f_ins == 1) && ( activ_f_pop == 1)){
if (id_frag == id_f_pop){
fragArray->pos[id_frag] = 0;
fragArray->start_bp[id_frag] = 0;
fragArray->len_bp[id_frag] = len_bp_f_pop;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = ori_f_pop;
fragArray->prev[id_frag] = -1;
fragArray->next[id_frag] = id_f_ins;
if (circ_f_ins == 0){
fragArray->id_c[id_frag] = max_id_contig + 1;
fragArray->l_cont[id_frag] = l_cont_f_ins - pos_f_ins + 1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_f_ins - start_bp_f_ins + len_bp_f_pop;
}
else{
fragArray->id_c[id_frag] = contig_f_ins;
fragArray->l_cont[id_frag] = l_cont_f_ins + 1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_f_ins + len_bp_f_pop;
}
fragArray->rep[id_frag] = o_fragArray->rep[id_frag];
fragArray->activ[id_frag] = o_fragArray->activ[id_frag];
fragArray->id_d[id_frag] = o_fragArray->id_d[id_frag];
}
else if ((id_frag < n_frags) && (id_frag != id_f_pop)){
int contig_fi = o_fragArray->id_c[id_frag];
int pos_fi = o_fragArray->pos[id_frag];
int l_cont_fi = o_fragArray->l_cont[id_frag];
int l_cont_bp_fi = o_fragArray->l_cont_bp[id_frag];
int len_bp_fi = o_fragArray->len_bp[id_frag];
int circ_fi = o_fragArray->circ[id_frag];
int id_prev_fi = o_fragArray->prev[id_frag];
int id_next_fi = o_fragArray->next[id_frag];
int start_bp_fi = o_fragArray->start_bp[id_frag];
int or_fi = o_fragArray->ori[id_frag];
int rep_fi = o_fragArray->rep[id_frag];
int activ_fi = o_fragArray->activ[id_frag];
int id_d_fi = o_fragArray->id_d[id_frag];
if (contig_fi == contig_f_ins){
if (circ_f_ins == 0){
if (pos_fi < pos_f_ins){
fragArray->pos[id_frag] = pos_fi;
fragArray->id_c[id_frag] = contig_f_ins;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = id_prev_fi;
if (pos_fi == (pos_f_ins -1)){
fragArray->next[id_frag] = -1;
}
else{
fragArray->next[id_frag] = id_next_fi;
}
fragArray->l_cont[id_frag] = pos_f_ins;
fragArray->l_cont_bp[id_frag] = start_bp_f_ins;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi == pos_f_ins){
fragArray->pos[id_frag] = 1;
fragArray->id_c[id_frag] = max_id_contig + 1;
fragArray->start_bp[id_frag] = len_bp_f_pop;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_f_ins;
fragArray->prev[id_frag] = id_f_pop;
fragArray->next[id_frag] = id_next_f_ins;
fragArray->l_cont[id_frag] = l_cont_f_ins - pos_f_ins + 1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_f_ins - start_bp_f_ins + len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi > pos_f_ins){
fragArray->pos[id_frag] = pos_fi - (pos_f_ins) + 1;
fragArray->id_c[id_frag] = max_id_contig + 1;
fragArray->start_bp[id_frag] = start_bp_fi - (start_bp_f_ins) + len_bp_f_pop;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = id_prev_fi;
fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_f_ins - pos_f_ins + 1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_f_ins - start_bp_f_ins + len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
else{ // contig_f_ins is circular
if (pos_fi < pos_f_ins){
fragArray->pos[id_frag] = l_cont_f_ins - pos_f_ins + pos_fi + 1;
fragArray->id_c[id_frag] = contig_f_ins;
fragArray->start_bp[id_frag] = l_cont_bp_f_ins - start_bp_f_ins + start_bp_fi + len_bp_f_pop;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = id_prev_fi;
if (pos_fi == pos_f_ins - 1){
fragArray->next[id_frag] = -1;
}
else{
fragArray->next[id_frag] = id_next_fi;
}
fragArray->l_cont[id_frag] = l_cont_f_ins + 1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_f_ins + len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi == pos_f_ins){
fragArray->pos[id_frag] = 1;
fragArray->id_c[id_frag] = contig_f_ins;
fragArray->start_bp[id_frag] = len_bp_f_pop;
fragArray->len_bp[id_frag] = len_bp_f_ins;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_f_ins;
fragArray->prev[id_frag] = id_f_pop;
fragArray->next[id_frag] = id_next_f_ins;
fragArray->l_cont[id_frag] = l_cont_f_ins + 1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_f_ins + len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi > pos_f_ins){
fragArray->pos[id_frag] = pos_fi - pos_f_ins + 1;
fragArray->id_c[id_frag] = contig_f_ins;
fragArray->start_bp[id_frag] = start_bp_fi - start_bp_f_ins + len_bp_f_pop;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = id_prev_fi;
if (id_frag == id_prev_f_ins){
fragArray->next[id_frag] = -1;
}
else{
fragArray->next[id_frag] = id_next_fi;
}
// fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_f_ins + 1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_f_ins + len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
}
else{
fragArray->pos[id_frag] = pos_fi;
fragArray->id_c[id_frag] = contig_fi;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = circ_fi;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = id_prev_fi;
fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_fi;
fragArray->l_cont_bp[id_frag] = l_cont_bp_fi;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
}
else{
if (id_frag < n_frags){
fragArray->pos[id_frag] = o_fragArray->pos[id_frag];
fragArray->id_c[id_frag] = o_fragArray->id_c[id_frag];
fragArray->circ[id_frag] = o_fragArray->circ[id_frag];
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = o_fragArray->ori[id_frag];
fragArray->start_bp[id_frag] = o_fragArray->start_bp[id_frag];
fragArray->len_bp[id_frag] = o_fragArray->len_bp[id_frag];
fragArray->prev[id_frag] = o_fragArray->prev[id_frag];
fragArray->next[id_frag] = o_fragArray->next[id_frag];
fragArray->l_cont[id_frag] = o_fragArray->l_cont[id_frag];
fragArray->l_cont_bp[id_frag] = o_fragArray->l_cont_bp[id_frag];
fragArray->rep[id_frag] = o_fragArray->rep[id_frag];
fragArray->activ[id_frag] = o_fragArray->activ[id_frag];
fragArray->id_d[id_frag] = o_fragArray->id_d[id_frag];
}
}
}
__global__ void pop_in_frag_2(frag* fragArray,frag* o_fragArray, int id_f_pop, int id_f_ins, int max_id_contig,
int ori_f_pop,
int n_frags)
{
// split insert @ right
__shared__ int contig_f_pop;
__shared__ int pos_f_pop;
__shared__ int l_cont_f_pop;
__shared__ int l_cont_bp_f_pop;
__shared__ int len_bp_f_pop;
__shared__ int start_bp_f_pop;
__shared__ int id_prev_f_pop;
__shared__ int id_next_f_pop;
__shared__ int activ_f_pop;
// __shared__ int or_f_pop;
__shared__ int contig_f_ins;
__shared__ int pos_f_ins;
__shared__ int l_cont_f_ins;
__shared__ int l_cont_bp_f_ins;
__shared__ int len_bp_f_ins;
__shared__ int start_bp_f_ins;
__shared__ int id_prev_f_ins;
__shared__ int id_next_f_ins;
__shared__ int circ_f_ins;
__shared__ int or_f_ins;
__shared__ int activ_f_ins;
int id_frag = threadIdx.x + blockDim.x * blockIdx.x;
if (threadIdx.x == 0){
contig_f_pop = o_fragArray->id_c[id_f_pop];
pos_f_pop = o_fragArray->pos[id_f_pop];
l_cont_f_pop = o_fragArray->l_cont[id_f_pop];
l_cont_bp_f_pop = o_fragArray->l_cont_bp[id_f_pop];
len_bp_f_pop = o_fragArray->len_bp[id_f_pop];
start_bp_f_pop = o_fragArray->start_bp[id_f_pop];
id_prev_f_pop = o_fragArray->prev[id_f_pop];
id_next_f_pop = o_fragArray->next[id_f_pop];
activ_f_pop = o_fragArray->activ[id_f_pop];
contig_f_ins = o_fragArray->id_c[id_f_ins];
pos_f_ins = o_fragArray->pos[id_f_ins];
l_cont_f_ins = o_fragArray->l_cont[id_f_ins];
l_cont_bp_f_ins = o_fragArray->l_cont_bp[id_f_ins];
len_bp_f_ins = o_fragArray->len_bp[id_f_ins];
start_bp_f_ins = o_fragArray->start_bp[id_f_ins];
id_prev_f_ins = o_fragArray->prev[id_f_ins];
id_next_f_ins = o_fragArray->next[id_f_ins];
circ_f_ins = o_fragArray->circ[id_f_ins];
or_f_ins = o_fragArray->ori[id_f_ins];
activ_f_ins = o_fragArray->activ[id_f_ins];
}
__syncthreads();
if ((activ_f_ins == 1) && ( activ_f_pop == 1)){
if (id_frag == id_f_pop){
if (circ_f_ins == 0){
fragArray->pos[id_frag] = pos_f_ins + 1;
fragArray->id_c[id_frag] = contig_f_ins;
fragArray->start_bp[id_frag] = start_bp_f_ins + len_bp_f_ins;
fragArray->len_bp[id_frag] = len_bp_f_pop;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = ori_f_pop;
fragArray->prev[id_frag] = id_f_ins;
fragArray->next[id_frag] = -1;
fragArray->l_cont[id_frag] = pos_f_ins + 2;
fragArray->l_cont_bp[id_frag] = start_bp_f_ins + len_bp_f_ins + len_bp_f_pop;
fragArray->rep[id_frag] = o_fragArray->rep[id_frag];
fragArray->activ[id_frag] = o_fragArray->activ[id_frag];
fragArray->id_d[id_frag] = o_fragArray->id_d[id_frag];
}
else{
fragArray->pos[id_frag] = (l_cont_f_ins - (pos_f_ins + 1)) + pos_f_ins + 1;
fragArray->id_c[id_frag] = contig_f_ins;
fragArray->start_bp[id_frag] = (l_cont_bp_f_ins - (start_bp_f_ins + len_bp_f_ins))
+ start_bp_f_ins + len_bp_f_ins;
fragArray->len_bp[id_frag] = len_bp_f_pop;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = ori_f_pop;
fragArray->prev[id_frag] = id_f_ins;
fragArray->next[id_frag] = -1;
fragArray->l_cont[id_frag] = l_cont_f_ins + 1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_f_ins + len_bp_f_pop;
fragArray->rep[id_frag] = o_fragArray->rep[id_frag];
fragArray->activ[id_frag] = o_fragArray->activ[id_frag];
fragArray->id_d[id_frag] = o_fragArray->id_d[id_frag];
}
}
else if ((id_frag < n_frags) && (id_frag != id_f_pop)){
int contig_fi = o_fragArray->id_c[id_frag];
int pos_fi = o_fragArray->pos[id_frag];
int l_cont_fi = o_fragArray->l_cont[id_frag];
int l_cont_bp_fi = o_fragArray->l_cont_bp[id_frag];
int len_bp_fi = o_fragArray->len_bp[id_frag];
int circ_fi = o_fragArray->circ[id_frag];
int id_prev_fi = o_fragArray->prev[id_frag];
int id_next_fi = o_fragArray->next[id_frag];
int start_bp_fi = o_fragArray->start_bp[id_frag];
int or_fi = o_fragArray->ori[id_frag];
int rep_fi = o_fragArray->rep[id_frag];
int activ_fi = o_fragArray->activ[id_frag];
int id_d_fi = o_fragArray->id_d[id_frag];
if (contig_fi == contig_f_ins){
if(circ_f_ins == 0){
if (pos_fi < pos_f_ins){
fragArray->pos[id_frag] = pos_fi;
fragArray->id_c[id_frag] = contig_f_ins;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
fragArray->prev[id_frag] = id_prev_fi;
fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = pos_f_ins + 2;
fragArray->l_cont_bp[id_frag] = start_bp_f_ins + len_bp_f_ins + len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi == pos_f_ins){
fragArray->pos[id_frag] = pos_fi;
fragArray->id_c[id_frag] = contig_f_ins;
fragArray->start_bp[id_frag] = start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_f_ins;
fragArray->prev[id_frag] = id_prev_f_ins;
fragArray->next[id_frag] = id_f_pop;
fragArray->l_cont[id_frag] = pos_f_ins + 2;
fragArray->l_cont_bp[id_frag] = start_bp_f_ins + len_bp_f_ins + len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi > pos_f_ins){
fragArray->pos[id_frag] = pos_fi - (pos_f_ins + 1);
fragArray->id_c[id_frag] = max_id_contig + 1;
fragArray->start_bp[id_frag] = start_bp_fi - (start_bp_f_ins + len_bp_f_ins);
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
if (pos_fi == (pos_f_ins + 1)){
fragArray->prev[id_frag] = -1;
}
else{
fragArray->prev[id_frag] = id_prev_fi;
}
fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_f_ins - (pos_f_ins + 1);
fragArray->l_cont_bp[id_frag] = l_cont_bp_f_ins - (start_bp_f_ins + len_bp_f_ins);
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
}
else{//circular contig
if (pos_fi < pos_f_ins){
fragArray->pos[id_frag] = (l_cont_f_ins - (pos_f_ins + 1)) + pos_fi;
fragArray->id_c[id_frag] = contig_f_ins;
fragArray->start_bp[id_frag] = (l_cont_bp_f_ins - (start_bp_f_ins + len_bp_f_ins))
+ start_bp_fi;
fragArray->len_bp[id_frag] = len_bp_fi;
fragArray->circ[id_frag] = 0;
fragArray->id[id_frag] = id_frag;
fragArray->ori[id_frag] = or_fi;
if (id_frag == id_next_f_ins){
fragArray->prev[id_frag] = -1;
}
else{
fragArray->prev[id_frag] = id_prev_fi;
}
// fragArray->prev[id_frag] = id_prev_fi;
fragArray->next[id_frag] = id_next_fi;
fragArray->l_cont[id_frag] = l_cont_f_ins + 1;
fragArray->l_cont_bp[id_frag] = l_cont_bp_f_ins + len_bp_f_pop;
fragArray->rep[id_frag] = rep_fi;
fragArray->activ[id_frag] = activ_fi;
fragArray->id_d[id_frag] = id_d_fi;
}
else if (pos_fi == pos_f_ins){