static void threadRoutine(void *para)
{
PARAMETER *prm;
unsigned int i;
unsigned char id;
prm = (PARAMETER *)para;
id = prm->threadID;
//printf("%dth thread with threadID %d, hash_table %p\n",id,prm.threadID,prm.hash_table);
while(1)
{
if(*(prm->selfSignal) == 1)
{
unsigned int seq_index = 0;
unsigned int pos = 0;
for(i = 0; i < kmer_c; i++)
{
if(seq_index < read_c && indexArray[seq_index + 1] == i)
{
seq_index++; // which sequence this kmer belongs to
pos = 0;
}
//if((unsigned char)(hashBanBuffer[i]&taskMask)!=id){
if((unsigned char)(hashBanBuffer[i] % thrd_num) != id)
{
pos++;
continue;
}
kmerCounter[id + 1]++;
singleKmer(i, KmerSets[id], seq_index, pos++);
}
*(prm->selfSignal) = 0;
}
else if(*(prm->selfSignal) == 2)
{
for(i = 0; i < read_c; i++)
{
if(i % thrd_num != id)
continue;
chopKmer4read(i, id + 1);
}
*(prm->selfSignal) = 0;
}
else if(*(prm->selfSignal) == 3)
{
*(prm->selfSignal) = 0;
break;
}
usleep(1);
}
}
static void threadRoutine ( void * para )
{
PARAMETER * prm;
int i;
unsigned char id;
prm = ( PARAMETER * ) para;
id = prm->threadID;
//printf("%dth thread with threadID %d, hash_table %p\n",id,prm.threadID,prm.hash_table);
while ( 1 )
{
if ( * ( prm->selfSignal ) == 1 )
{
for ( i = 0; i < kmer_c; i++ )
{
//if((unsigned char)(magic_seq(hashBanBuffer[i])%thrd_num)!=id)
//if((kmerBuffer[i]%thrd_num)!=id)
if ( ( hashBanBuffer[i] % thrd_num ) != id )
{ continue; }
kmerCounter[id + 1]++;
singleKmer ( i, KmerSets[id] );
}
* ( prm->selfSignal ) = 0;
}
else if ( * ( prm->selfSignal ) == 2 )
{
for ( i = 0; i < read_c; i++ )
{
if ( i % thrd_num != id )
{ continue; }
chopKmer4read ( i, id + 1 );
}
* ( prm->selfSignal ) = 0;
}
else if ( * ( prm->selfSignal ) == 3 )
{
* ( prm->selfSignal ) = 0;
break;
}
else if ( * ( prm->selfSignal ) == 4 )
{
thread_mark ( KmerSets[id], id );
* ( prm->selfSignal ) = 0;
}
else if ( * ( prm->selfSignal ) == 5 )
{
thread_delow ( KmerSets[id], id );
* ( prm->selfSignal ) = 0;
}
usleep ( 1 );
}
}
// 2 -> 1 -> 3 -> 4 -> 6
static void threadRoutine (void *para)
{
PARAMETER *prm;
int i, t, j, start, finish;
unsigned char id;
prm = (PARAMETER *) para;
id = prm->threadID;
//printf("%dth thread with task %d, hash_table %p\n",id,prm.task,prm.hash_table);
while (1)
{
if (*(prm->selfSignal) == 1)
{
for (i = 0; i < kmer_c; i++)
{
//if((hashBanBuffer[i]&taskMask)!=prm.threadID)
if ((hashBanBuffer[i] % thrd_num) != id)
{
continue;
}
searchKmer (i, KmerSets[id]);
}
*(prm->selfSignal) = 0;
}
else if (*(prm->selfSignal) == 2)
{
for (i = 0; i < read_c; i++)
{
if (i % thrd_num != id)
{
continue;
}
chopKmer4read (i, id + 1);
}
*(prm->selfSignal) = 0;
}
else if (*(prm->selfSignal) == 3)
{
// parse reads
for (t = 0; t < read_c; t++)
{
if (t % thrd_num != id)
{
continue;
}
parse1read (t, id + 1);
}
*(prm->selfSignal) = 0;
}
else if (*(prm->selfSignal) == 4)
{
//printf("thread %d, reads %d splay kmerplus\n",id,read_c);
for (t = 0; t < read_c; t++)
{
start = indexArray[t];
finish = indexArray[t + 1];
for (j = start; j < finish; j++)
{
if (flagArray[j] == 0)
{
#ifdef MER127
if(mixBuffer[j].low2==0)
#endif
#ifdef MER63
if(mixBuffer[j].low==0)
#endif
#ifdef MER31
if(mixBuffer[j]==0)
#endif
{
break;
}
}
else if (hashBanBuffer[j] % thrd_num == id)
{
//fprintf(stderr,"thread %d search for ban %lld\n",id,hashBanBuffer[j]);
search1kmerPlus (j, id);
}
/*
if(flagArray[j]==0&&mixBuffer[j]==0)
break;
if(!flagArray[j]||(hashBanBuffer[j]%thrd_num)!=id)
continue;
search1kmerPlus(j,id);
*/
}
}
*(prm->selfSignal) = 0;
}
else if (*(prm->selfSignal) == 6)
{
for (t = 0; t < read_c; t++)
{
start = indexArray[t];
finish = indexArray[t + 1];
for (j = start; j < finish - 1; j++)
{
#ifdef MER127
if (mixBuffer[j].low2 == 0 || mixBuffer[j + 1].low2 == 0)
{
break;
}
if (mixBuffer[j].low2 % thrd_num != id)
{
continue;
}
thread_add1preArc (mixBuffer[j].low2, mixBuffer[j + 1].low2, id);
#endif
#ifdef MER63
if (mixBuffer[j].low == 0 || mixBuffer[j + 1].low == 0)
{
break;
}
if (mixBuffer[j].low % thrd_num != id)
{
continue;
}
thread_add1preArc (mixBuffer[j].low, mixBuffer[j + 1].low, id);
#endif
#ifdef MER31
if (mixBuffer[j] == 0 || mixBuffer[j + 1] == 0)
{
break;
}
if (mixBuffer[j] % thrd_num != id)
{
continue;
}
thread_add1preArc (mixBuffer[j], mixBuffer[j + 1], id);
#endif
}
}
*(prm->selfSignal) = 0;
}
else if (*(prm->selfSignal) == 5)
{
*(prm->selfSignal) = 0;
break;
}
usleep (1);
}
}
