void createCntMemManager()
{
if ( !cn_mem_manager )
{ cn_mem_manager = createMem_manager ( CNBLOCKSIZE, sizeof ( CONNECT ) ); }
else
{ printf ( "cn_mem_manger was created\n" ); }
}
void createRVmemo()
{
if ( !rv_mem_manager )
{ rv_mem_manager = createMem_manager ( RVBLOCKSIZE, sizeof ( READINTERVAL ) ); }
else
{ printf ( "Warning from createRVmemo: rv_mem_manager is an active pointer\n" ); }
}
void createCntMemManager ()
{
if ( !cn_mem_manager )
{
cn_mem_manager = createMem_manager ( CNBLOCKSIZE, sizeof ( CONNECT ) );
}
else
{
fprintf ( stderr, "The cn_mem_manger created.\n" );
}
}
void prlRead2edge (char *libfile, char *outfile)
{
char *cach1;
char *cach2;
unsigned char asm_ctg = 1;
long long i;
char name[256], *src_name, *next_name;
FILE *outfp = NULL;
int maxReadNum, libNo;
boolean flag, pairs = 0;
pthread_t threads[thrd_num];
unsigned char thrdSignal[thrd_num + 1];
PARAMETER paras[thrd_num];
maxReadLen = 0;
maxNameLen = 256;
scan_libInfo (libfile);
alloc_pe_mem (num_libs);
if (!maxReadLen)
{
maxReadLen = 100;
}
maxReadLen4all = maxReadLen;
printf ("In file: %s, max seq len %d, max name len %d\n\n", libfile, maxReadLen, maxNameLen);
if (repsTie)
{
sprintf (name, "%s.path", outfile);
outfp = ckopen (name, "wb");
}
src_name = (char *) ckalloc ((maxNameLen + 1) * sizeof (char));
next_name = (char *) ckalloc ((10*maxNameLen + 1) * sizeof (char));
kmerBuffer = (Kmer *) ckalloc (buffer_size * sizeof (Kmer));
mixBuffer = (Kmer *) ckalloc (buffer_size * sizeof (Kmer));
hashBanBuffer = (ubyte8 *) ckalloc (buffer_size * sizeof (ubyte8));
nodeBuffer = (kmer_t **) ckalloc (buffer_size * sizeof (kmer_t *));
smallerBuffer = (boolean *) ckalloc (buffer_size * sizeof (boolean));
flagArray = (boolean *) ckalloc (buffer_size * sizeof (boolean));
maxReadNum = buffer_size / (maxReadLen - overlaplen + 1);
//printf("buffer for at most %d reads\n",maxReadNum);
int maxAIOSize = 32768;/*
aioBuffer1 = (char *) ckalloc ((maxAIOSize) * sizeof (char));
aioBuffer2 = (char *) ckalloc ((maxAIOSize) * sizeof (char));
readBuffer1 = (char *) ckalloc ((maxAIOSize + 1024) * sizeof (char)); //(char *)ckalloc(maxAIOSize*sizeof(char));
readBuffer2 = (char *) ckalloc ((maxAIOSize + 1024) * sizeof (char));
cach1 = (char *) ckalloc (1024 * sizeof (char));
cach2 = (char *) ckalloc (1024 * sizeof (char));
memset(cach1,'\0',1024);
memset(cach2,'\0',1024);*/
aioBuffer1 = (char *) ckalloc ((maxAIOSize) * sizeof (char));
aioBuffer2 = (char *) ckalloc ((maxAIOSize) * sizeof (char));
readBuffer1 = (char *) ckalloc ((maxAIOSize + (maxReadLen+1024)) * sizeof (char)); //(char *)ckalloc(maxAIOSize*sizeof(char)); //1024
readBuffer2 = (char *) ckalloc ((maxAIOSize + (maxReadLen+1024)) * sizeof (char)); //1024
cach1 = (char *) ckalloc ((maxReadLen+1024) * sizeof (char)); //1024
cach2 = (char *) ckalloc ((maxReadLen+1024) * sizeof (char)); //1024
memset(cach1,'\0',(maxReadLen+1024)); //1024
memset(cach2,'\0',(maxReadLen+1024)); //1024
seqBuffer = (char **) ckalloc (maxReadNum * sizeof (char *));
lenBuffer = (int *) ckalloc (maxReadNum * sizeof (int));
indexArray = (int *) ckalloc ((maxReadNum + 1) * sizeof (int));
for (i = 0; i < maxReadNum; i++)
{
seqBuffer[i] = (char *) ckalloc (maxReadLen * sizeof (char));
}
memoAlloc4preArc ();
flags = (char **) ckalloc ((thrd_num + 1) * sizeof (char *));
deletion = (int *) ckalloc ((thrd_num + 1) * sizeof (int));
rcSeq = (char **) ckalloc ((thrd_num + 1) * sizeof (char *));
if (repsTie)
{
markerOnEdge = (unsigned char *) ckalloc ((num_ed + 1) * sizeof (unsigned char));
for (i = 1; i <= num_ed; i++)
{
markerOnEdge[i] = 0;
}
fwriteBuf = (unsigned int *) ckalloc ((maxReadLen - overlaplen + 1) * sizeof (unsigned int));
}
thrdSignal[0] = 0;
if (1)
{
preArc_mem_managers = (MEM_MANAGER **) ckalloc (thrd_num * sizeof (MEM_MANAGER *));
arcCounters = (unsigned int *) ckalloc (thrd_num * sizeof (unsigned int));
for (i = 0; i < thrd_num; i++)
{
arcCounters[i] = 0;
preArc_mem_managers[i] = createMem_manager (preARCBLOCKSIZE, sizeof (preARC));
deletion[i + 1] = 0;
flags[i + 1] = (char *) ckalloc (2 * maxReadLen * sizeof (char));
rcSeq[i + 1] = (char *) ckalloc (maxReadLen * sizeof (char));
thrdSignal[i + 1] = 0;
paras[i].threadID = i;
paras[i].mainSignal = &thrdSignal[0];
paras[i].selfSignal = &thrdSignal[i + 1];
}
creatThrds (threads, paras);
}
if (1)
{
deletion[0] = 0;
flags[0] = (char *) ckalloc (2 * maxReadLen * sizeof (char));
rcSeq[0] = (char *) ckalloc (maxReadLen * sizeof (char));
}
kmer_c = n_solexa = read_c = i = libNo = readNumBack = gradsCounter = 0;
int t0, t1, t2, t3, t4, t5, t6;
t0 = t1 = t2 = t3 = t4 = t5 = t6 = 0;
time_t read_start, read_end, time_bef, time_aft;
time (&read_start);
while (openNextFile (&libNo, pairs, asm_ctg))
{
if (lib_array[libNo].curr_type == 4)
{
int type = 0; //deside the PE reads is good or bad
while ((flag = read1seqInLibBam (seqBuffer[read_c], next_name, &(lenBuffer[read_c]), &libNo, pairs, 1, &type)) != 0)
{
if (type == -1) //if the reads is bad, go back.
{
i--;
if (lenBuffer[read_c - 1] >= overlaplen + 1)
{
kmer_c -= lenBuffer[read_c - 1] - overlaplen + 1;
read_c--;
}
n_solexa -= 2;
continue;
}
if ((++i) % 1000000 == 0)
{
printf ("--- %lldth reads\n", i);
}
if (lenBuffer[read_c] < overlaplen + 1)
{
continue;
}
//if(lenBuffer[read_c]>70)
// lenBuffer[read_c] = 70;
//else if(lenBuffer[read_c]>40)
// lenBuffer[read_c] = 40;
indexArray[read_c] = kmer_c;
kmer_c += lenBuffer[read_c] - overlaplen + 1;
read_c++;
if (read_c == maxReadNum)
{
indexArray[read_c] = kmer_c;
time (&read_end);
t0 += read_end - read_start;
time (&time_bef);
sendWorkSignal (2, thrdSignal);
time (&time_aft);
t1 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (1, thrdSignal);
time (&time_aft);
t2 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (3, thrdSignal);
time (&time_aft);
t3 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (4, thrdSignal);
time (&time_aft);
t4 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (6, thrdSignal);
time (&time_aft);
t5 += time_aft - time_bef;
time (&time_bef);
//recordPreArc();
if (repsTie)
{
recordPathBin (outfp);
}
time (&time_aft);
t6 += time_aft - time_bef;
//output_path(read_c,edge_no,flags,outfp);
kmer_c = 0;
read_c = 0;
time (&read_start);
}
}
}
else if (lib_array[libNo].curr_type == 1 || lib_array[libNo].curr_type == 2)
{
initAIO (&aio1, aioBuffer1, fileno (lib_array[libNo].fp1), maxAIOSize);
initAIO (&aio2, aioBuffer2, fileno (lib_array[libNo].fp2), maxAIOSize);
int offset1, offset2, flag1, flag2, rt1, rt2;
offset1 = offset2 = 0;
rt1 = aio_read (&aio1);
rt2 = aio_read (&aio2);
flag1 = AIORead (&aio1, &offset1, readBuffer1, cach1, &rt1, lib_array[libNo].curr_type);
flag2 = AIORead (&aio2, &offset2, readBuffer2, cach2, &rt2, lib_array[libNo].curr_type);
if(flag1 && flag2)
{
int start1, start2, turn;
start1 = start2 = 0;
turn = 1;
while (start1 < offset1 || start2 < offset2)
{
if (turn == 1)
{
turn = 2;
readseqInLib (seqBuffer[read_c], next_name, &(lenBuffer[read_c]), readBuffer1, &start1, offset1, libNo);
if ((++i) % 1000000 == 0)
printf ("--- %lldth reads\n", i);
/* if (lenBuffer[read_c] < overlaplen + 1)
continue;*/
if (lenBuffer[read_c] < overlaplen + 1)
{
if(start1>=offset1)
{
start1=0;
flag1=AIORead (&aio1, &offset1, readBuffer1, cach1, &rt1, lib_array[libNo].curr_type);
}
continue;
}
indexArray[read_c] = kmer_c;
kmer_c += lenBuffer[read_c] - overlaplen + 1;
read_c++;
if(start1>=offset1){
start1=0;
flag1=AIORead (&aio1, &offset1, readBuffer1, cach1, &rt1, lib_array[libNo].curr_type);
}
if (read_c == maxReadNum) {
indexArray[read_c] = kmer_c;
time (&read_end);
t0 += read_end - read_start;
time (&time_bef);
sendWorkSignal (2, thrdSignal);
time (&time_aft);
t1 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (1, thrdSignal);
time (&time_aft);
t2 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (3, thrdSignal);
time (&time_aft);
t3 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (4, thrdSignal);
time (&time_aft);
t4 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (6, thrdSignal);
time (&time_aft);
t5 += time_aft - time_bef;
time (&time_bef);
//recordPreArc();
if (repsTie)
recordPathBin (outfp);
time (&time_aft);
t6 += time_aft - time_bef;
//output_path(read_c,edge_no,flags,outfp);
kmer_c = 0;
read_c = 0;
time (&read_start);
}
continue;
}
if (turn == 2)
{
turn = 1;
readseqInLib (seqBuffer[read_c], next_name, &(lenBuffer[read_c]), readBuffer2, &start2, offset2, libNo);
if ((++i) % 1000000 == 0)
printf ("--- %lldth reads\n", i);
/* if (lenBuffer[read_c] < overlaplen + 1)
continue;*/
if (lenBuffer[read_c] < overlaplen + 1)
{
if((flag2 == 2) && (start2 >= offset2))
break;
if(start2 >= offset2)
{
start2=0;
flag2 = AIORead (&aio2, &offset2, readBuffer2, cach2, &rt2, lib_array[libNo].curr_type);
}
continue;
}
indexArray[read_c] = kmer_c;
kmer_c += lenBuffer[read_c] - overlaplen + 1;
read_c++;
if((flag2 == 2) && (start2 >= offset2))
break;
if(start2 >= offset2){
start2=0;
flag2 = AIORead (&aio2, &offset2, readBuffer2, cach2, &rt2, lib_array[libNo].curr_type);
}
if (read_c == maxReadNum){
indexArray[read_c] = kmer_c;
time (&read_end);
t0 += read_end - read_start;
time (&time_bef);
sendWorkSignal (2, thrdSignal);
time (&time_aft);
t1 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (1, thrdSignal);
time (&time_aft);
t2 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (3, thrdSignal);
time (&time_aft);
t3 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (4, thrdSignal);
time (&time_aft);
t4 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (6, thrdSignal);
time (&time_aft);
t5 += time_aft - time_bef;
time (&time_bef);
//recordPreArc();
if (repsTie)
recordPathBin (outfp);
time (&time_aft);
t6 += time_aft - time_bef;
//output_path(read_c,edge_no,flags,outfp);
kmer_c = 0;
read_c = 0;
time (&read_start);
}
continue;
}
}
}
}
else
{
initAIO (&aio1, aioBuffer1, fileno (lib_array[libNo].fp1), maxAIOSize);
int offset, flag1, rt;
offset = 0;
rt = aio_read (&aio1);
while ((flag1 = AIORead (&aio1, &offset, readBuffer1, cach1, &rt, lib_array[libNo].curr_type)))
{
int start = 0;
while (start < offset)
{
readseqInLib (seqBuffer[read_c], next_name, &(lenBuffer[read_c]), readBuffer1, &start, offset, libNo);
if ((++i) % 1000000 == 0)
printf ("--- %lld reads\n", i);
if (lenBuffer[read_c] < overlaplen + 1)
continue;
indexArray[read_c] = kmer_c;
kmer_c += lenBuffer[read_c] - overlaplen + 1;
read_c++;
if (read_c > maxReadNum - 1024)
{
indexArray[read_c] = kmer_c;
time (&read_end);
t0 += read_end - read_start;
time (&time_bef);
sendWorkSignal (2, thrdSignal);
time (&time_aft);
t1 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (1, thrdSignal);
time (&time_aft);
t2 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (3, thrdSignal);
time (&time_aft);
t3 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (4, thrdSignal);
time (&time_aft);
t4 += time_aft - time_bef;
time (&time_bef);
sendWorkSignal (6, thrdSignal);
time (&time_aft);
t5 += time_aft - time_bef;
time (&time_bef);
//recordPreArc();
if (repsTie)
recordPathBin (outfp);
time (&time_aft);
t6 += time_aft - time_bef;
//output_path(read_c,edge_no,flags,outfp);
kmer_c = 0;
read_c = 0;
time (&read_start);
}
}
if (flag1 == 2)
break;
}
}
}
printf ("%lld reads processed\n", i);
printf ("time %d,%d,%d,%d,%d,%d,%d\n", t0, t1, t2, t3, t4, t5, t6);
if (read_c)
{
indexArray[read_c] = kmer_c;
sendWorkSignal (2, thrdSignal);
sendWorkSignal (1, thrdSignal);
sendWorkSignal (3, thrdSignal);
sendWorkSignal (4, thrdSignal);
sendWorkSignal (6, thrdSignal);
//recordPreArc();
if (repsTie)
{
recordPathBin (outfp);
}
}
printf ("%lld markers outputed\n", markCounter);
sendWorkSignal (5, thrdSignal);
thread_wait (threads);
output_arcs (outfile);
memoFree4preArc ();
if (1) // multi-threads
{
arcCounter = 0;
for (i = 0; i < thrd_num; i++)
{
arcCounter += arcCounters[i];
free ((void *) flags[i + 1]);
deletion[0] += deletion[i + 1];
free ((void *) rcSeq[i + 1]);
}
}
if (1)
{
free ((void *) flags[0]);
free ((void *) rcSeq[0]);
}
printf ("done mapping reads, %d reads deleted, %lld arcs created\n", deletion[0], arcCounter);
if (repsTie)
{
free ((void *) markerOnEdge);
free ((void *) fwriteBuf);
}
free ((void *) arcCounters);
free ((void *) rcSeq);
for (i = 0; i < maxReadNum; i++)
{
free ((void *) seqBuffer[i]);
}
free ((void *) seqBuffer);
free ((void *) lenBuffer);
free ((void *) indexArray);
free ((void *) flags);
free ((void *) deletion);
free ((void *) kmerBuffer);
free ((void *) mixBuffer);
free ((void *) smallerBuffer);
free ((void *) flagArray);
free ((void *) hashBanBuffer);
free ((void *) nodeBuffer);
free ((void *) src_name);
free ((void *) next_name);
free ((void *) aioBuffer1);
free ((void *) aioBuffer2);
free ((void *) readBuffer1);
free ((void *) readBuffer2);
free ((void *) cach1);
free ((void *) cach2);
if (repsTie)
{
fclose (outfp);
}
free_pe_mem ();
free_libs ();
}