static void serpent_encrypt(const uint32_t in_blk[4], uint32_t out_blk[], const uint32_t *l_key)
{
uint32_t a,b,c,d,e,f,g,h;
uint32_t t1,t2,t3,t4,t5,t6,t7,t8,t9,t10,t11,t12,t13,t14,t15,t16;
#ifdef BLOCK_SWAP
a = byteswap32(in_blk[3]); b = byteswap32(in_blk[2]);
c = byteswap32(in_blk[1]); d = byteswap32(in_blk[0]);
#else
a = in_blk[0]; b = in_blk[1]; c = in_blk[2]; d = in_blk[3];
#endif
k_xor( 0,a,b,c,d); sb0(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor( 1,e,f,g,h); sb1(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor( 2,a,b,c,d); sb2(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor( 3,e,f,g,h); sb3(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor( 4,a,b,c,d); sb4(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor( 5,e,f,g,h); sb5(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor( 6,a,b,c,d); sb6(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor( 7,e,f,g,h); sb7(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor( 8,a,b,c,d); sb0(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor( 9,e,f,g,h); sb1(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(10,a,b,c,d); sb2(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(11,e,f,g,h); sb3(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(12,a,b,c,d); sb4(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(13,e,f,g,h); sb5(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(14,a,b,c,d); sb6(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(15,e,f,g,h); sb7(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(16,a,b,c,d); sb0(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(17,e,f,g,h); sb1(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(18,a,b,c,d); sb2(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(19,e,f,g,h); sb3(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(20,a,b,c,d); sb4(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(21,e,f,g,h); sb5(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(22,a,b,c,d); sb6(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(23,e,f,g,h); sb7(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(24,a,b,c,d); sb0(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(25,e,f,g,h); sb1(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(26,a,b,c,d); sb2(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(27,e,f,g,h); sb3(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(28,a,b,c,d); sb4(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(29,e,f,g,h); sb5(e,f,g,h,a,b,c,d); rot(a,b,c,d);
k_xor(30,a,b,c,d); sb6(a,b,c,d,e,f,g,h); rot(e,f,g,h);
k_xor(31,e,f,g,h); sb7(e,f,g,h,a,b,c,d); k_xor(32,a,b,c,d);
#ifdef BLOCK_SWAP
out_blk[3] = byteswap32(a); out_blk[2] = byteswap32(b);
out_blk[1] = byteswap32(c); out_blk[0] = byteswap32(d);
#else
out_blk[0] = a; out_blk[1] = b; out_blk[2] = c; out_blk[3] = d;
#endif
};
void abcFilterSNP::run(funkyPars *pars){
if(!doSnpStat)
return;
chunkyT *chk = pars->chk;
if(doSnpStat==1){
kstring_t *bufstr = new kstring_t;
bufstr->s=NULL;bufstr->l=bufstr->m=0;
//loop over sites;
for(int s=0;s<pars->numSites;s++){
if(pars->keepSites[s]==0)
continue;
//loop over samples
int cnts[4]={0,0,0,0};
for(int i=0;i<pars->nInd;i++){
tNode *nd = chk->nd[s][i];
if(nd==NULL)
continue;
for(int l=0;l<nd->l;l++){
int obB = refToInt[nd->seq[l]];
// fprintf(stderr,"%c ",nd.seq[l]);
int strand = (isupper(nd->seq[l])==0)<<1;
// fprintf(stderr,"strand:%d\n",strand);
if(obB==4)
continue;
if((obB!=pars->major[s] && obB!=pars->minor[s]) )
continue;
if(obB!=pars->major[s])
strand +=1;
//fprintf(stderr,"strand=%d\n",strand);
cnts[strand]++;
}
}
ksprintf(bufstr,"%s\t%d\t%d %d %d %d\t",header->target_name[pars->refId],pars->posi[s]+1, cnts[0],cnts[1],cnts[2],cnts[3]);
ksprintf(bufstr,"%f:%f:%f\t",sb1(cnts),sb2(cnts),sb3(cnts));
funkyHWE *hweStruct = (funkyHWE *) pars->extras[8];//THIS IS VERY NASTY! the ordering within general.cpp is now important
double lrt = 2*hweStruct->like0[s]-2*hweStruct->likeF[s];
double pval;
if(lrt<0)
pval =1;
else
pval =1- chi.cdf(lrt);
ksprintf(bufstr,"%f:%e\t",lrt,pval);
double Z = baseQbias(chk->nd[s],pars->nInd,refToInt[pars->major[s]],refToInt[pars->minor[s]]);
ksprintf(bufstr,"%f:%e\n",Z,2*phi(Z));
}
pars->extras[index] = bufstr;
}
}
void testRedraw() {
FrameBuffer fb;
fb.backgroundColor = (Color(255, 255, 255));
fb.clear();
ShadowBuffer sb(fb.width, fb.height, 0, 0, fb.finfo.line_length);
sb.backgroundColor = Color(50, 50, 50);
ShadowBuffer sb2(sb.width - 100, sb.height, 0, 0, fb.finfo.line_length);
sb2.backgroundColor = (Color(100, 100, 100));
ShadowBuffer sb3(200, 200, 1166, 0, fb.finfo.line_length);
sb3.backgroundColor = (Color(0, 0, 0));
sb3.clear();
sb.shadows.push_back(&sb2);
sb.shadows.push_back(&sb3);
for (int j = 0; j < 50; j++) {
sb.clear();
sb2.clear();
//START create boxes
for (int i = 0; i < 50; i++) {
Color c(rand() % 255, rand() % 255, rand() % 255);
int offsetX = rand() % sb2.width;
int offsetY = rand() % sb2.height;
for (int y = 0; y < 100; y++) {
for (int x = 0; x < 100; x++) {
sb2.plot(offsetX + x, offsetY + y, c);
}
}
}
sb3.offsetX -= 2;
sb3.offsetY += 4;
//END create boxes
sb.draw();
fb.draw(sb);
}
}