static struct mafAli *getRefAli(char *database, char *chrom, int start, int end)
{
struct mafAli *ali;
struct mafComp *comp;
char buffer[1024];
AllocVar(ali);
AllocVar(comp);
ali->components = comp;
ali->textSize = end - start;
safef(buffer, sizeof buffer, "%s.%s", database, chrom);
comp->src = cloneString(buffer);
comp->start = start;
comp->strand = '+';
comp->size = end - start;
struct dnaSeq *seq = hChromSeqMixed(database, chrom, start , end);
comp->text = cloneString(seq->dna);
freeDnaSeq(&seq);
return ali;
}
void ultraPcrRegions(char *database, char *bedFile, char *outFa)
/* ultraPcrRegions - Get regions to PCR up and some surrounding sequence. */
{
int extraSize = 1000;
FILE *f = mustOpen(outFa, "w");
struct bed *bed, *bedList = bedLoadNAll(bedFile, 4);
hSetDb(database);
for (bed = bedList; bed != NULL; bed = bed->next)
{
int bedSize = bed->chromEnd - bed->chromStart;
int chromSize = hChromSize(bed->chrom);
int seqSize;
int seqStart = bed->chromStart - extraSize;
int seqEnd = bed->chromEnd + extraSize;
int firstParenPos, secondParenPos;
struct dyString *dy;
char fileName[512];
struct dnaSeq *seq;
if (seqStart < 0)
seqStart = 0;
if (seqEnd > chromSize)
seqEnd = chromSize;
seqSize = seqEnd - seqStart;
firstParenPos = bed->chromStart - seqStart;
secondParenPos = firstParenPos + bedSize;
seq = hChromSeqMixed(bed->chrom, seqStart, seqEnd);
dy = dyStringNew(seqSize+2);
dyStringAppendN(dy, seq->dna, firstParenPos);
dyStringAppendC(dy, '(');
dyStringAppendN(dy, seq->dna+firstParenPos, secondParenPos-firstParenPos);
dyStringAppendC(dy, ')');
dyStringAppendN(dy, seq->dna+secondParenPos, seqSize - secondParenPos);
faWriteNext(f, bed->name, dy->string, dy->stringSize);
}
carefulClose(&f);
}
