void doItBigWig(struct inInfo *in, struct bed *chiaList, struct bigWigValsOnChrom *chromVals,
double *out1, double *out2)
{
struct bed *chromStart, *chromEnd, *chia;
int chiaIx = 0;
for (chromStart = chiaList; chromStart != NULL; chromStart = chromEnd)
{
chromEnd = bedListNextDifferentChrom(chromStart);
if (bigWigValsOnChromFetchData(chromVals, chromStart->chrom, in->bbi))
{
for (chia = chromStart; chia != chromEnd; chia = chia->next)
{
int blockStart = chia->chromStart;
int blockSize = chia->blockSizes[0];
out1[chiaIx] = averageInRegion(chromVals, blockStart, blockSize);
blockStart = chia->chromStart + chia->chromStarts[1];
blockSize = chia->blockSizes[1];
out2[chiaIx] = averageInRegion(chromVals, blockStart, blockSize);
++chiaIx;
}
}
else
{
/* No data on this chrom, just output zero everywhere. */
for (chia = chromStart; chia != chromEnd; chia = chia->next)
{
out1[chiaIx] = out2[chiaIx] = 0;
++chiaIx;
}
}
verboseDot();
}
}
void doDots(int *pDotMod)
/* Output a dot every now and then. */
{
if (dots > 0)
{
if (--*pDotMod <= 0)
{
verboseDot();
*pDotMod = dots;
}
}
}
static void itsaFillInTraverseArray(char *dna, bits32 *suffixArray, bits32 arraySize,
bits32 *traverseArray, UBYTE *cursorArray)
/* Fill in the bits that will help us traverse the array as if it were a tree. */
{
int depth = 0;
int stackSize = 4*1024;
int *stack;
AllocArray(stack, stackSize);
bits32 i;
for (i=0; i<arraySize; ++i)
{
char *curDna = dna + suffixArray[i];
int d;
for (d = 0; d<depth; ++d)
{
bits32 prevIx = stack[d];
char *prevDna = dna + suffixArray[prevIx];
if (curDna[d] != prevDna[d])
{
int stackIx;
for (stackIx=d; stackIx<depth; ++stackIx)
{
prevIx = stack[stackIx];
traverseArray[prevIx] = i - prevIx;
}
depth = d;
break;
}
}
if (depth >= stackSize)
errAbort("Stack overflow, depth >= %d", stackSize);
stack[depth] = i;
cursorArray[i] = depth; // May overflow. That's ok. We just care about indexed ones which are < 13.
depth += 1;
if ((i&0xFFFFF)==0xFFFFF)
{
verboseDot();
if ((i&0x3FFFFFF)==0)
verbose(1, "traversed %lld%%\n", 100LL*i/arraySize);
}
}
verbose(1, "finished traversal\n");
/* Do final clear out of stack */
int stackIx;
for (stackIx=0; stackIx < depth; ++stackIx)
{
bits32 prevIx = stack[stackIx];
traverseArray[prevIx] = arraySize - prevIx;
}
}
static void itsaWriteMerged(struct chromInfo *chromList, DNA *allDna,
bits32 *offsetArray, bits32 *listArray, bits32 *index13, char *output)
/* Write out a file that contains a single splix that is the merger of
* all of the individual splixes in list. As a side effect will replace
* offsetArray with suffix array and listArray with traverse array */
{
FILE *f = mustOpen(output, "w+");
/** Allocate header and fill out easy constant fields. */
struct itsaFileHeader *header;
AllocVar(header);
header->majorVersion = ITSA_MAJOR_VERSION;
header->minorVersion = ITSA_MINOR_VERSION;
/* Figure out sizes of names and sequence for each chromosome. */
struct chromInfo *chrom;
bits32 chromNamesSize = 0;
bits64 dnaDiskSize = 1; /* For initial zero. */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
chromNamesSize += strlen(chrom->name) + 1;
dnaDiskSize += chrom->size + 1; /* Include separating zeroes. */
}
/* Fill in most of rest of header fields */
header->chromCount = slCount(chromList);
header->chromNamesSize = roundUpTo4(chromNamesSize);
header->dnaDiskSize = roundUpTo4(dnaDiskSize);
bits32 chromSizesSize = header->chromCount*sizeof(bits32);
/* Write header. */
mustWrite(f, header, sizeof(*header));
/* Write chromosome names. */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
mustWrite(f, chrom->name, strlen(chrom->name)+1);
zeroPad(f, header->chromNamesSize - chromNamesSize);
/* Write chromosome sizes. */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
mustWrite(f, &chrom->size, sizeof(chrom->size));
int chromSizesSizePad = chromSizesSize - header->chromCount * sizeof(bits32);
zeroPad(f, chromSizesSizePad);
/* Write out chromosome DNA and zeros before, between, and after. */
mustWrite(f, allDna, dnaDiskSize);
zeroPad(f, header->dnaDiskSize - dnaDiskSize);
verboseTime(1, "Wrote %lld bases of DNA including zero padding", header->dnaDiskSize);
/* Calculate and write suffix array. Convert index13 to index of array as opposed to index
* of sequence. */
bits64 arraySize = 0;
off_t suffixArrayFileOffset = ftello(f);
int slotCount = itsaSlotCount;
int slotIx;
for (slotIx=0; slotIx < slotCount; ++slotIx)
{
int slotSize = finishAndWriteOneSlot(offsetArray, listArray, index13[slotIx], allDna, f);
/* Convert index13 to hold the position in the suffix array where the first thing matching
* the corresponding 13-base prefix is found. */
if (slotSize != 0)
index13[slotIx] = arraySize+1; /* The +1 is so we can keep 0 for not found. */
else
index13[slotIx] = 0;
arraySize += slotSize;
if ((slotIx % 200000 == 0) && slotIx != 0)
{
verboseDot();
if (slotIx % 10000000 == 0)
verbose(1, "fine sort bucket %d of %d\n", slotIx, slotCount);
}
}
verbose(1, "fine sort bucket %d of %d\n", slotCount, slotCount);
verboseTime(1, "Wrote %lld suffix array positions", arraySize);
/* Now we're done with the offsetArray and listArray buffers, so use them for the
* next phase. */
bits32 *suffixArray = offsetArray;
offsetArray = NULL; /* Help make some errors more obvious */
bits32 *traverseArray = listArray;
listArray = NULL; /* Help make some errors more obvious */
/* Read the suffix array back from the file. */
fseeko(f, suffixArrayFileOffset, SEEK_SET);
mustRead(f, suffixArray, arraySize*sizeof(bits32));
verboseTime(1, "Read suffix array back in");
/* Calculate traverse array and cursor arrays */
memset(traverseArray, 0, arraySize*sizeof(bits32));
UBYTE *cursorArray = needHugeMem(arraySize);
itsaFillInTraverseArray(allDna, suffixArray, arraySize, traverseArray, cursorArray);
verboseTime(1, "Filled in traverseArray");
/* Write out traverse array. */
mustWrite(f, traverseArray, arraySize*sizeof(bits32));
verboseTime(1, "Wrote out traverseArray");
/* Write out 13-mer index. */
mustWrite(f, index13, itsaSlotCount*sizeof(bits32));
verboseTime(1, "Wrote out index13");
/* Write out bits of cursor array corresponding to index. */
for (slotIx=0; slotIx<itsaSlotCount; ++slotIx)
{
bits32 indexPos = index13[slotIx];
if (indexPos == 0)
fputc(0, f);
else
fputc(cursorArray[indexPos-1], f);
}
verboseTime(1, "Wrote out cursors13");
/* Update a few fields in header, and go back and write it out again with
* the correct magic number to indicate it's complete. */
header->magic = ITSA_MAGIC;
header->arraySize = arraySize;
header->size = sizeof(*header) // header
+ header->chromNamesSize + // chromosome names
+ header->chromCount * sizeof(bits32) // chromosome sizes
+ header->dnaDiskSize // dna sequence
+ sizeof(bits32) * arraySize // suffix array
+ sizeof(bits32) * arraySize // traverse array
+ sizeof(bits32) * itsaSlotCount // index13
+ sizeof(UBYTE) * itsaSlotCount; // cursors13
rewind(f);
mustWrite(f, header, sizeof(*header));
carefulClose(&f);
verbose(1, "Completed %s is %lld bytes\n", output, header->size);
}
void hierSort(char *inputList)
/* Do a hierarchical merge sort so we don't run out of system file handles */
{
int level = 0;
char thisName[256];
char nextName[256];
char sortName[256];
struct lineFile *thisLf = NULL;
FILE *nextF = NULL;
int sortCount = 0;
FILE *sortF = NULL;
int fileCount = 0;
char *files[MAXFILES];
boolean more = FALSE;
int block=0;
char *line=NULL;
safef(nextName, sizeof(nextName), "%s", inputList);
do
{
block=0;
safef(thisName, sizeof(thisName), "%s", nextName);
safef(nextName, sizeof(nextName), "%sinputList%d-", tempDir, level+1);
makeTempName(&tempName, nextName, ".tmp");
safef(nextName, sizeof(nextName), "%s", tempName.forCgi);
thisLf = lineFileOpen(thisName,TRUE);
if (!thisLf)
errAbort("error lineFileOpen(%s) returned NULL\n",thisName);
more = lineFileNext(thisLf, &line, NULL);
while (more)
{
int i=0;
fileCount = 0;
while (more && fileCount < MAXFILES)
{
files[fileCount++]=cloneString(line);
more = lineFileNext(thisLf, &line, NULL);
}
if (!more && block==0)
{ /* last level */
sortF = stdout;
}
else
{
if (!nextF)
nextF = mustOpen(nextName,"w");
safef(sortName, sizeof(sortName), "%ssort%d-", tempDir, sortCount++);
makeTempName(&tempName, sortName, ".tmp");
safef(sortName, sizeof(sortName), "%s", tempName.forCgi);
fprintf(nextF, "%s\n", sortName);
sortF = mustOpen(sortName,"w");
}
chainMergeSort(fileCount, files, sortF, level);
if (sortF != stdout)
carefulClose(&sortF);
for(i=0;i<fileCount;++i)
freez(&files[i]);
verboseDot();
verbose(2,"block=%d\n",block);
++block;
}
lineFileClose(&thisLf);
if (nextF)
carefulClose(&nextF);
if (level > 0)
{
remove(thisName);
}
verbose(1,"\n");
verbose(2,"level=%d, block=%d\n",level,block);
++level;
} while (block > 1);
}
void averageFetchingEachChrom(struct bbiFile *bbi, struct bed **pBedList, int fieldCount,
FILE *f, FILE *bedF)
/* Do the averaging by sorting bedList by chromosome, and then processing each chromosome
* at once. Faster for long bedLists. */
{
/* Sort by chromosome. */
slSort(pBedList, bedCmpChrom);
struct bigWigValsOnChrom *chromVals = bigWigValsOnChromNew();
struct bed *bed, *bedList, *nextChrom;
verbose(1, "processing chromosomes");
for (bedList = *pBedList; bedList != NULL; bedList = nextChrom)
{
/* Figure out which chromosome we're working on, and the last bed using it. */
char *chrom = bedList->chrom;
nextChrom = nextChromInList(bedList);
verbose(2, "Processing %s\n", chrom);
if (bigWigValsOnChromFetchData(chromVals, chrom, bbi))
{
double *valBuf = chromVals->valBuf;
Bits *covBuf = chromVals->covBuf;
/* Loop through beds doing sums and outputting. */
for (bed = bedList; bed != nextChrom; bed = bed->next)
{
int size = 0, coverage = 0;
double sum = 0.0;
if (sampleAroundCenter > 0)
{
int center = (bed->chromStart + bed->chromEnd)/2;
int left = center - (sampleAroundCenter/2);
addBufIntervalInfo(valBuf, covBuf, left, left+sampleAroundCenter,
&size, &coverage, &sum);
}
else
{
if (fieldCount < 12)
{
addBufIntervalInfo(valBuf, covBuf, bed->chromStart, bed->chromEnd,
&size, &coverage, &sum);
}
else
{
int i;
for (i=0; i<bed->blockCount; ++i)
{
int start = bed->chromStart + bed->chromStarts[i];
int end = start + bed->blockSizes[i];
addBufIntervalInfo(valBuf, covBuf, start, end, &size, &coverage, &sum);
}
}
}
/* Print out result, fudging mean to 0 if no coverage at all. */
double mean = 0;
if (coverage > 0)
mean = sum/coverage;
fprintf(f, "%s\t%d\t%d\t%g\t%g\t%g\n", bed->name, size, coverage, sum, sum/size, mean);
optionallyPrintBedPlus(bedF, bed, fieldCount, mean);
}
verboseDot();
}
else
{
/* If no bigWig data on this chromosome, just output as if coverage is 0 */
for (bed = bedList; bed != nextChrom; bed = bed->next)
{
fprintf(f, "%s\t%d\t0\t0\t0\t0\n", bed->name, bedTotalBlockSize(bed));
optionallyPrintBedPlus(bedF, bed, fieldCount, 0);
}
}
}
verbose(1, "\n");
}
/* Core algorithm */
int cluster (FILE *fw, Edge **el, int n)
{
int block_id = 0;
Block **bb;
int allocated = po->SCH_BLOCK;
AllocArray(bb, allocated);
Edge *e;
Block *b;
struct dyStack *genes, *scores, *b_genes, *allincluster;
int i, j, k, components;
AllocArray(profile, cols);
for (j = 0; j < cols; j++)
AllocArray(profile[j], sigma);
genes = dsNew(rows);
scores = dsNew(rows);
allincluster = dsNew(rows);
bool *candidates;
AllocArray(candidates, rows);
e = *el;
i = 0;
while (i++ < n)
{
/*printf ("%d\n",i);*/
e = *el++;
/* check if both genes already enumerated in previous blocks */
bool flag = TRUE;
/* speed up the program if the rows bigger than 200 */
if (rows > 250)
{
if ( isInStack(allincluster,e->gene_one) && isInStack(allincluster,e->gene_two) )
flag = FALSE;
else if ((po->IS_TFname)&&(e->gene_one!= TFindex)&&(e->gene_two!=TFindex))
flag = FALSE;
else if ((po->IS_list)&&(!sublist[e->gene_one] || !sublist[e->gene_two]))
flag =FALSE;
}
else
{
flag = check_seed(e, bb, block_id);
if ((po->IS_TFname)&&(e->gene_one!= TFindex)&&(e->gene_two!=TFindex))
flag = FALSE;
if ((po->IS_list)&&(!sublist[e->gene_one] || !sublist[e->gene_two]))
flag = FALSE;
}
if (!flag) continue;
for (j = 0; j < cols; j++)
for (k = 0; k < sigma; k++)
profile[j][k] = 0;
/*you must allocate a struct if you want to use the pointers related to it*/
AllocVar(b);
/*initial the b->score*/
b->score = MIN(2, e->score);
/* initialize the stacks genes and scores */
int ii;
dsClear(genes);
dsClear(scores);
for(ii = 0; ii < rows; ii ++)
{
dsPush(genes,-1);
dsPush(scores,-1);
}
dsClear(genes);
dsClear(scores);
/*printf ("%d\t%d\n",e->gene_one,e->gene_two);*/
dsPush(genes, e->gene_one);
dsPush(genes, e->gene_two);
dsPush(scores, 1);
dsPush(scores, b->score);
/* branch-and-cut condition for seed expansion */
int cand_threshold = floor(po->COL_WIDTH * po->TOLERANCE);
if (cand_threshold < 2)
cand_threshold = 2;
/* maintain a candidate list to avoid looping through all rows */
for (j = 0; j < rows; j++)
candidates[j] = TRUE;
candidates[e->gene_one] = candidates[e->gene_two] = FALSE;
components = 2;
/* expansion step, generate a bicluster without noise */
block_init(e, b, genes, scores, candidates, cand_threshold, &components, allincluster);
/* track back to find the genes by which we get the best score*/
for(k = 0; k < components; k++)
{
/* printf ("******%d\t%d\n",dsItem(scores,k),b->score);*/
if ((dsItem(scores,k) == b->score)&&(dsItem(scores,k+1)!= b->score)) break;
}
components = k + 1;
/*printf ("%d",components);*/
int ki;
for (ki=0; ki < rows; ki++)
candidates[ki] = TRUE;
for (ki=0; ki < components - 1 ; ki++)
{
seed_update(arr_c[dsItem(genes,ki)]);
candidates[dsItem(genes,ki)] = FALSE;
}
candidates[dsItem(genes,k)] = FALSE;
genes->top = k ;
int cnt = 0;
bool *colcand;
AllocArray(colcand, cols);
for(ki = 0; ki < cols; ki++)
colcand[ki] = FALSE;
/* add columns satisfy the conservative r */
seed_current_modify(arr_c[dsItem(genes,k)], colcand, &cnt, components);
/* add some new possible genes */
int m_cnt=0;
continuous KL_score=0;
discrete *sub_array;
for ( ki = 0; ki < rows; ki++)
{
if (po->IS_list && !sublist[ki]) continue;
m_cnt = intersect_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt* po->TOLERANCE)) )
{
sub_array = get_intersect_row(colcand,arr_c[dsItem(genes,0)],arr_c[ki],m_cnt);
KL_score = get_KL (sub_array, arr_c[ki], m_cnt, cols);
/*printf ("%d\t%.2f\n",m_cnt,KL_score);*/
if (KL_score>=b->significance * po->TOLERANCE)
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
}
b->block_rows_pre = components;
/* add genes that negative regulated to the consensus */
for ( ki = 0; ki < rows; ki++)
{
if (po->IS_list && !sublist[ki]) continue;
m_cnt = reverse_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt * po->TOLERANCE)) )
{
sub_array = get_intersect_reverse_row(colcand,arr_c[dsItem(genes,0)],arr_c[ki],m_cnt);
KL_score = get_KL (sub_array, arr_c[ki], m_cnt, cols);
if (KL_score>=b->significance * po->TOLERANCE)
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
}
free(colcand);
/* save the current cluster*/
b_genes = dsNew(b->block_rows_pre);
for (ki = 0; ki < b->block_rows_pre; ki++)
dsPush(b_genes, dsItem(genes,ki));
/* store gene arrays inside block */
b->genes = dsNew(components);
b->conds = dsNew(cols);
scan_block(b_genes, b);
if (b->block_cols == 0) continue;
b->block_rows = components;
b->score = b->score;
/* b->score = b->block_rows * b->block_cols; */
dsClear(b->genes);
for ( ki=0; ki < components; ki++)
dsPush(b->genes,dsItem(genes,ki));
for(ki = 0; ki < components; ki++)
if(!isInStack(allincluster, dsItem(genes,ki)))
dsPush(allincluster,dsItem(genes,ki));
/*save the current block b to the block list bb so that we can sort the blocks by their score*/
bb[block_id++] = b;
/* reaching the results number limit */
if (block_id == po->SCH_BLOCK) break;
verboseDot();
}
/* writes character to the current position in the standard output (stdout) and advances the internal file position indicator to the next position.
* It is equivalent to putc(character,stdout).*/
putchar('\n');
/* free-up the candidate list */
free(candidates);
free(allincluster);
block_enrichment(fw, bb, block_id);
return report_blocks(fw, bb, block_id);
}
void pslSort2(char *outFile, char *tempDir)
/* Do second step of sort - merge all sorted files in tempDir
* to final. */
{
char fileName[512];
struct slName *tmpList, *tmp;
struct midFile *midList = NULL, *mid;
int aliCount = 0;
FILE *f = mustOpen(outFile, "w");
if (!nohead)
pslWriteHead(f);
tmpList = listDir(tempDir, "tmp*.psl");
if (tmpList == NULL)
errAbort("No tmp*.psl files in %s\n", tempDir);
for (tmp = tmpList; tmp != NULL; tmp = tmp->next)
{
sprintf(fileName, "%s/%s", tempDir, tmp->name);
AllocVar(mid);
mid->lf = pslFileOpen(fileName);
slAddHead(&midList, mid);
}
verbose(1, "writing %s", outFile);
fflush(stdout);
/* Write out the lowest sorting line from mid list until done. */
for (;;)
{
struct midFile *bestMid = NULL;
if ( (++aliCount & 0xffff) == 0)
{
verboseDot();
fflush(stdout);
}
for (mid = midList; mid != NULL; mid = mid->next)
{
if (mid->lf != NULL && mid->psl == NULL)
{
if ((mid->psl = nextPsl(mid->lf)) == NULL)
lineFileClose(&mid->lf);
}
if (mid->psl != NULL)
{
if (bestMid == NULL || pslCmpQuery(&mid->psl, &bestMid->psl) < 0)
bestMid = mid;
}
}
if (bestMid == NULL)
break;
pslTabOut(bestMid->psl, f);
pslFree(&bestMid->psl);
}
printf("\n");
fclose(f);
/* The followint really shouldn't be necessary.... */
for (mid = midList; mid != NULL; mid = mid->next)
lineFileClose(&mid->lf);
printf("Cleaning up temp files\n");
for (tmp = tmpList; tmp != NULL; tmp = tmp->next)
{
sprintf(fileName, "%s/%s", tempDir, tmp->name);
remove(fileName);
}
}
/* Core algorithm */
int cluster (FILE *fw, Edge **el, int n)
{
int block_id = 0;
Block **bb;
int allocated = po->SCH_BLOCK;
AllocArray(bb, allocated);
Edge *e;
Block *b;
struct dyStack *genes, *scores, *b_genes, *allincluster;
int i, j, k, components;
AllocArray(profile, cols);
for (j = 0; j < cols; j++) AllocArray(profile[j], sigma);
genes = dsNew(rows);
scores = dsNew(rows);
allincluster = dsNew(rows);
bool *candidates;
AllocArray(candidates, rows);
e = *el; i = 0;
while (i++ < n)
{
e = *el++;
/*printf("a:%d b:%d score:%d\n",e->gene_one,e->gene_two,e->score);*/
/* check if both genes already enumerated in previous blocks */
bool flag = TRUE;
/* speed up the program if the rows bigger than 200 */
if (rows > 200)
{
if ( isInStack(allincluster,e->gene_one) && isInStack(allincluster,e->gene_two) )
flag = FALSE;
}
else
{
flag = check_seed(e, bb, block_id);
}
if (!flag) continue;
for (j = 0; j < cols; j++)
for (k = 0; k < sigma; k++) profile[j][k] = 0;
AllocVar(b);
b->score = MIN(2, e->score);
/* initialize the stacks genes and scores */
int ii;
dsClear(genes);
dsClear(scores);
for(ii = 0; ii < rows; ii ++)
{
dsPush(genes,-1);
dsPush(scores,-1);
}
dsClear(genes);
dsClear(scores);
dsPush(genes, e->gene_one);
dsPush(genes, e->gene_two);
dsPush(scores, 1);
dsPush(scores, b->score);
/* branch-and-cut condition for seed expansion */
int cand_threshold = floor(po->COL_WIDTH * po->TOLERANCE);
if (cand_threshold < 2) cand_threshold = 2;
/* maintain a candidate list to avoid looping through all rows */
for (j = 0; j < rows; j++) candidates[j] = TRUE;
candidates[e->gene_one] = candidates[e->gene_two] = FALSE;
components = 2;
/* expansion step, generate a bicluster without noise */
block_init(e, b, genes, scores, candidates, cand_threshold, &components, allincluster);
/* track back to find the best score that which genes makes it */
for(k = 0; k < components; k++)
if ((dsItem(scores,k) == b->score)&&(dsItem(scores,k+1)!= b->score)) break;
components = k + 1;
int ki;
for (ki=0; ki < rows; ki++)
candidates[ki] = TRUE;
for (ki=0; ki < components - 1 ; ki++)
{
seed_update(arr_c[dsItem(genes,ki)]);
candidates[dsItem(genes,ki)] = FALSE;
}
candidates[dsItem(genes,k)] = FALSE;
genes->top = k ;
int cnt = 0;
bool *colcand;
AllocArray(colcand, cols);
for(ki = 0; ki < cols; ki++) colcand[ki] = FALSE;
/* add columns satisfy the conservative r */
seed_current_modify(arr_c[dsItem(genes,k)], colcand, &cnt, components);
/* add some new possible genes */
int m_cnt;
for ( ki = 0; ki < rows; ki++)
{
m_cnt = intersect_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt* po->TOLERANCE)) )
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
b->block_rows_pre = components;
/* add genes that negative regulated to the consensus */
for ( ki = 0; ki < rows; ki++)
{
m_cnt = reverse_row(colcand, arr_c[dsItem(genes,0)], arr_c[ki]);
if ( candidates[ki] && (m_cnt >= floor(cnt * po->TOLERANCE)) )
{
dsPush(genes,ki);
components++;
candidates[ki] = FALSE;
}
}
free(colcand);
/* save the current cluster*/
b_genes = dsNew(b->block_rows_pre);
for (ki = 0; ki < b->block_rows_pre; ki++)
dsPush(b_genes, dsItem(genes,ki));
/* store gene arrays inside block */
b->genes = dsNew(components);
b->conds = dsNew(cols);
scan_block(b_genes, b);
if (b->block_cols == 0) continue;
b->block_rows = components;
b->score = b->block_rows * b->block_cols;
dsClear(b->genes);
for ( ki=0; ki < components; ki++)
dsPush(b->genes,dsItem(genes,ki));
for(ki = 0; ki < components; ki++)
if(!isInStack(allincluster, dsItem(genes,ki))) dsPush(allincluster,dsItem(genes,ki));
bb[block_id++] = b;
/* reaching the results number limit */
if (block_id == po->SCH_BLOCK) break;
verboseDot();
}
putchar('\n');
/* free-up the candidate list */
free(candidates);
free(allincluster);
return report_blocks(fw, bb, block_id);
}
void bigWigMerge(int inCount, char *inFiles[], char *outFile)
/* bigWigMerge - Merge together multiple bigWigs into a single one.. */
{
/* Make a list of open bigWig files. */
struct bbiFile *inFile, *inFileList = NULL;
int i;
for (i=0; i<inCount; ++i)
{
if (clInList)
{
addWigsInFile(inFiles[i], &inFileList);
}
else
{
inFile = bigWigFileOpen(inFiles[i]);
slAddTail(&inFileList, inFile);
}
}
FILE *f = mustOpen(outFile, "w");
struct bbiChromInfo *chrom, *chromList = getAllChroms(inFileList);
verbose(1, "Got %d chromosomes from %d bigWigs\nProcessing",
slCount(chromList), slCount(inFileList));
double *mergeBuf = NULL;
int mergeBufSize = 0;
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
struct lm *lm = lmInit(0);
/* Make sure merge buffer is big enough. */
int chromSize = chrom->size;
verboseDot();
verbose(2, "Processing %s (%d bases)\n", chrom->name, chromSize);
if (chromSize > mergeBufSize)
{
mergeBufSize = chromSize;
freeMem(mergeBuf);
mergeBuf = needHugeMem(mergeBufSize * sizeof(double));
}
int i;
for (i=0; i<chromSize; ++i)
mergeBuf[i] = 0.0;
/* Loop through each input file grabbing data and merging it in. */
for (inFile = inFileList; inFile != NULL; inFile = inFile->next)
{
struct bbiInterval *ivList = bigWigIntervalQuery(inFile, chrom->name, 0, chromSize, lm);
verbose(3, "Got %d intervals in %s\n", slCount(ivList), inFile->fileName);
struct bbiInterval *iv;
for (iv = ivList; iv != NULL; iv = iv->next)
{
double val = iv->val;
if (val > clClip)
val = clClip;
int end = iv->end;
for (i=iv->start; i < end; ++i)
mergeBuf[i] += val;
}
}
/* Output each range of same values as a bedGraph item */
int sameCount;
for (i=0; i<chromSize; i += sameCount)
{
sameCount = doublesTheSame(mergeBuf+i, chromSize-i);
double val = mergeBuf[i] + clAdjust;
if (val > clThreshold)
fprintf(f, "%s\t%d\t%d\t%g\n", chrom->name, i, i + sameCount, val);
}
lmCleanup(&lm);
}
verbose(1, "\n");
carefulClose(&f);
}
