static void makeOligoHistogram(char *fileName, struct seqList *seqList,
int oligoSize, int **retTable, int *retTotal)
/* Make up table of oligo occurences. Either pass in an FA file or a seqList.
* (the other should be NULL). */
{
FILE *f = NULL;
int tableSize = (1<<(oligoSize+oligoSize));
int tableByteSize = tableSize * sizeof(int);
int *table = needLargeMem(tableByteSize);
struct dnaSeq *seq;
struct seqList *seqEl = seqList;
int *softMask = NULL;
int total = 0;
if (seqList == NULL)
f = mustOpen(fileName, "rb");
memset(table, 0, tableByteSize);
for (;;)
{
DNA *dna;
int size;
int endIx;
int i;
int oliVal;
if (seqList != NULL)
{
if (seqEl == NULL)
break;
seq = seqEl->seq;
softMask = seqEl->softMask;
seqEl = seqEl->next;
}
else
{
seq = faReadOneDnaSeq(f, "", TRUE);
if (seq == NULL)
break;
}
dna = seq->dna;
size = seq->size;
endIx = size-oligoSize;
for (i=0; i<=endIx; ++i)
{
if (softMask == NULL || !masked(softMask+i, oligoSize) )
{
if ((oliVal = oligoVal(dna+i, oligoSize)) >= 0)
{
table[oliVal] += 1;
++total;
}
}
}
if (seqList == NULL)
freeDnaSeq(&seq);
}
carefulClose(&f);
*retTable = table;
*retTotal = total;
}
struct dnaSeq *nextWormCdna(struct wormCdnaIterator *it)
/* Return next sequence in database */
{
return faReadOneDnaSeq(it->faFile, "unknown", TRUE);
}
