void pslToChain(char *pslIn, char *chainOut)
/* pslToChain - Extract multiple psl records. */
{
struct lineFile *lf = pslFileOpen(pslIn);
int chainId = 1;
int ii;
FILE *f = mustOpen(chainOut, "w");
struct psl *psl;
struct chain chain;
while ((psl = pslNext(lf) ) != NULL)
{
if (psl->strand[1] == '-')
{
if (ignoreError)
continue;
errAbort("PSL record on line %d has '-' for target strand which is not allowed.", lf->lineIx);
}
chain.score = pslScore(psl);
chain.id = chainId++;
chain.tName = psl->tName;
chain.tSize = psl->tSize;
chain.tStart = psl->tStart;
chain.tEnd = psl->tEnd;
chain.qName = psl->qName;
chain.qSize = psl->qSize;
chain.qStrand = psl->strand[0];
if (psl->strand[0] == '-')
{
chain.qEnd = psl->qSize - psl->qStart;
chain.qStart = psl->qSize - psl->qEnd;
}
else
{
chain.qStart = psl->qStart;
chain.qEnd = psl->qEnd;
}
chainWriteHead(&chain,f);
for(ii=0; ii < psl->blockCount; ii++)
{
fprintf(f, "%d", psl->blockSizes[ii]);
if (ii < psl->blockCount - 1)
fprintf(f, "\t%d\t%d", psl->tStarts[ii+1]-(psl->tStarts[ii] + psl->blockSizes[ii]),
psl->qStarts[ii+1]-(psl->qStarts[ii] + psl->blockSizes[ii]));
fprintf(f,"\n");
}
pslFree(&psl);
}
}
void chainWrite(struct chain *chain, FILE *f)
/* Write out chain to file in usual format*/
{
struct cBlock *b, *nextB;
chainWriteHead(chain, f);
for (b = chain->blockList; b != NULL; b = nextB)
{
nextB = b->next;
fprintf(f, "%d", b->qEnd - b->qStart);
if (nextB != NULL)
fprintf(f, "\t%d\t%d",
nextB->tStart - b->tEnd, nextB->qStart - b->qEnd);
fputc('\n', f);
}
fputc('\n', f);
}
