static boolean checkSnapOk(struct vertex *vOld, struct vertex *vNew, boolean isRev,
int bleedSize, int maxUncheckedSize, struct nibTwoCache *seqCache, char *chromName)
/* Load sequence that corresponds to bleed-over, and make sure that sequence of next
* exon is similar. */
{
if (vertexPartOfUncuttableEdge(vOld, isRev))
return FALSE;
if (bleedSize <= maxUncheckedSize)
return TRUE;
int minScore = bleedSize-2;
boolean similar = FALSE;
if (isRev)
{
int oldStart = vOld->position;
struct slRef *eRef;
struct dnaSeq *oldSeq = nibTwoCacheSeqPartExt(seqCache, chromName, oldStart, bleedSize, FALSE, NULL);
for (eRef = vNew->waysIn; eRef != NULL; eRef = eRef->next)
{
struct edge *edge = eRef->val;
struct vertex *vRest = edge->start;
int newStart = vRest->position - bleedSize;
struct dnaSeq *newSeq = nibTwoCacheSeqPartExt(seqCache, chromName, newStart, bleedSize, FALSE, NULL);
similar = checkSeqSimilar(oldSeq, newSeq, minScore);
dnaSeqFree(&newSeq);
if (similar)
break;
}
dnaSeqFree(&oldSeq);
}
else
{
int oldStart = vOld->position - bleedSize;
struct slRef *eRef;
struct dnaSeq *oldSeq = nibTwoCacheSeqPartExt(seqCache, chromName, oldStart, bleedSize, FALSE, NULL);
for (eRef = vNew->waysOut; eRef != NULL; eRef = eRef->next)
{
struct edge *edge = eRef->val;
struct vertex *vRest = edge->end;
int newStart = vRest->position;
struct dnaSeq *newSeq = nibTwoCacheSeqPartExt(seqCache, chromName, newStart, bleedSize, FALSE, NULL);
similar = checkSeqSimilar(oldSeq, newSeq, minScore);
dnaSeqFree(&newSeq);
if (similar)
break;
}
}
return similar;
}
struct dnaSeq *nibTwoCacheSeqPart(struct nibTwoCache *ntc, char *seqName, int start, int size,
int *retFullSeqSize)
/* Return part of sequence. If *retFullSeqSize is non-null then return full size of
* sequence (not just loaded part) there. This will have repeats in lower case. */
{
return nibTwoCacheSeqPartExt(ntc, seqName, start, size, TRUE, retFullSeqSize);
}
static struct dnaSeq *seqReaderGet(struct seqReader *seqReader, char *seqName, int start, int end,
int *retFullSeqSize)
/* return part of a sequence from a seqReader. dnaSeqFree result when
* complete. */
{
assert(start <= end);
if (seqReader->nibTwo != NULL)
return nibTwoCacheSeqPartExt(seqReader->nibTwo, seqName, start, end-start, gMasked, retFullSeqSize);
else
return seqReaderTblGet(seqReader, seqName, start, end, retFullSeqSize);
}
struct dnaSeq *loadSeqStrand(struct nibTwoCache *ntc, char *seqName, int start, int end,
char strand)
/* Load in a mixed case sequence, from reverse strand if
* strand is '-'. */
{
struct dnaSeq *seq;
int size = end - start;
assert(size >= 0);
if (strand == '-')
{
reverseIntRange(&start, &end, nibTwoGetSize(ntc, seqName));
seq = nibTwoCacheSeqPartExt(ntc, seqName, start, size, TRUE, NULL);
reverseComplement(seq->dna, seq->size);
}
else
{
seq = nibTwoCacheSeqPartExt(ntc, seqName, start, size, TRUE, NULL);
}
return seq;
}