void boundSearchTest( )
{
TEST_INIT;
int maxSize = 1024*256;
int bucketSize = 256;
b3OpenCLArray<b3SortData> srcCL(g_context,g_queue,maxSize);
b3OpenCLArray<unsigned int> upperCL(g_context,g_queue,maxSize);
b3OpenCLArray<unsigned int> lowerCL(g_context,g_queue,maxSize);
b3AlignedObjectArray<b3SortData> srcHost;
b3AlignedObjectArray<unsigned int> upperHost;
b3AlignedObjectArray<unsigned int> lowerHost;
b3AlignedObjectArray<unsigned int> upperHostCompare;
b3AlignedObjectArray<unsigned int> lowerHostCompare;
b3BoundSearchCL* search = new b3BoundSearchCL(g_context,g_device,g_queue, maxSize);
int dx = maxSize/NUM_TESTS;
for(int iter=0; iter<NUM_TESTS; iter++)
{
int size = b3Min( 128+dx*iter, maxSize );
upperHost.resize(bucketSize);
lowerHost.resize(bucketSize);
upperHostCompare.resize(bucketSize);
lowerHostCompare.resize(bucketSize);
srcHost.resize(size);
for(int i=0; i<size; i++)
{
b3SortData v;
// v.m_key = i<2? 0 : 5;
v.m_key = getRandom(0,bucketSize);
v.m_value = i;
srcHost.at(i) = v;
}
srcHost.quickSort(b3SortDataCompare());
srcCL.copyFromHost(srcHost);
{
for(int i=0; i<bucketSize; i++)
{
lowerHost[i] = -1;
lowerHostCompare[i] = -1;
upperHost[i] = -1;
upperHostCompare[i] = -1;
}
upperCL.copyFromHost(upperHost);
lowerCL.copyFromHost(lowerHost);
}
search->execute(srcCL,size,upperCL,bucketSize,b3BoundSearchCL::BOUND_UPPER);
search->execute(srcCL,size,lowerCL,bucketSize,b3BoundSearchCL::BOUND_LOWER);
search->executeHost(srcHost,size,upperHostCompare,bucketSize,b3BoundSearchCL::BOUND_UPPER);
search->executeHost(srcHost,size,lowerHostCompare,bucketSize,b3BoundSearchCL::BOUND_LOWER);
lowerCL.copyToHost(lowerHost);
upperCL.copyToHost(upperHost);
for(int i=0; i<bucketSize; i++)
{
TEST_ASSERT(upperHostCompare[i] == upperHost[i]);
TEST_ASSERT(lowerHostCompare[i] == lowerHost[i]);
}
/*
for(int i=1; i<bucketSize; i++)
{
int lhi_1 = lowerHost[i-1];
int lhi = lowerHost[i];
for(int j=lhi_1; j<lhi; j++)
//for(int j=lowerHost[i-1]; j<lowerHost[i]; j++)
{
TEST_ASSERT( srcHost[j].m_key < i );
}
}
for(int i=0; i<bucketSize; i++)
{
int jMin = (i==0)?0:upperHost[i-1];
for(int j=jMin; j<upperHost[i]; j++)
{
TEST_ASSERT( srcHost[j].m_key <= i );
}
}
*/
for(int i=0; i<bucketSize; i++)
{
int lhi = lowerHost[i];
int uhi = upperHost[i];
for(int j=lhi; j<uhi; j++)
{
if ( srcHost[j].m_key != i )
{
printf("error %d != %d\n",srcHost[j].m_key,i);
}
TEST_ASSERT( srcHost[j].m_key == i );
}
}
}
delete search;
TEST_REPORT( "boundSearchTest" );
}
void scanFile(Args *args, FILE *fp){
char *line, *name, *token, *chr;
size_t n;
int status, len, l, start, end;
int pos[2], p, i, tp, tn;
Data *data;
double ll, ul, cf;
line = NULL;
while((status = getline(&line,&n,fp)) != -1){
if(line[0] != '#')
break;
}
if(!args->p)
printf("# Int\tChr\tStart\tEnd\tLen\t[%%\t%%\t%%]\t[cM/Mb\tcM/Mb\tcM/Mb]\n");
data = newData(1,args->o);
while(status != -1){
data->n = 0;
name = estrdup(strtok(line,"\t")); /* read name of region */
chr = estrdup(strtok(NULL,"\t")); /* read chromosome */
start = intVal(strtok(NULL,"\t")); /* start position */
end = intVal(strtok(NULL,"\t")); /* end position */
len = end - start + 1; /* length of region in bp */
tp = 0; /* total positives */
tn = 0; /* total negatives */
while((token = strtok(NULL,"\t")) != NULL){ /* iterating across experiments */
if(data->n + 1 == data->maxN)
expandData(data);
l = strlen(token);
p = 0;
for(i=0;i<l;i++){ /* determine positions of commata */
if(token[i] == '|'){
token[i] = '\0';
pos[p++] = i+1;
}
}
data->numMol[data->n] = atoi(token); /* number of molecules */
token += pos[0];
data->numPos[data->n] = atoi(token);
token -= pos[0];
token += pos[1];
data->numNeg[data->n] = atoi(token);
token -= pos[1];
tp += data->numPos[data->n];
tn += data->numNeg[data->n];
data->n++;
}
if(args->d){
printData(name,len,data);
exit(0);
}
if(args->p && tp){
printLikFun(data, args);
return;
}
cf = crossoverFreq(data);
data->mlXover = cf;
data->ci = args->c;
ul = upperCL(data,cf);
ll = lowerCL(data,cf);
/* convert to centi-Morgans */
ll *= 100;
cf *= 100;
ul *= 100;
if(cf < 100){
printf("%s\t%s\t%d\t%d\t%*d\t%.3f\t%.3f\t%.3f",name,chr,start,end,4,len,ll,cf,ul);
/* convert to cM per Mb */
ll = ll / len * 1000000;
cf = cf / len * 1000000;
ul = ul / len * 1000000;
printf("\t%.3f\t%.3f\t%.3f\n",ll,cf,ul);
}else
printf("%s\t%d\t%d\t%*d\tNA\tNA\tNA\tNA\tNA\tNA\n",name,start,end,4,len);
status = getline(&line,&n,fp);
free(name);
}
free(line);
freeData(data);
}
