void copyPslXaToTab(char *pslFile, char *tabFile)
/* copy a single PSL XA to the tab file */
{
struct xAli *xa;
char *row[23];
struct lineFile *lf = lineFileOpen(pslFile, TRUE);
struct pipeline *pl = NULL;
FILE *tabFh = NULL;
if (noSort)
tabFh = mustOpen(tabFile, "w");
else
{
if (pslCreateOpts & PSL_WITH_BIN)
pl = pipelineOpen(outPipeBin, pipelineWrite, tabFile, NULL);
else
pl = pipelineOpen(outPipeNoBin, pipelineWrite, tabFile, NULL);
tabFh = pipelineFile(pl);
}
while (lineFileRow(lf, row))
{
xa = xAliLoad(row);
if (pslCreateOpts & PSL_WITH_BIN)
fprintf(tabFh, "%u\t", hFindBin(xa->tStart, xa->tEnd));
xAliTabOut(xa, tabFh);
xAliFree(&xa);
}
lineFileClose(&lf);
if (noSort)
carefulClose(&tabFh);
else
{
pipelineWait(pl);
pipelineFree(&pl);
}
}
void liftPsl(char *destFile, struct hash *liftHash, int sourceCount, char *sources[],
boolean querySide, boolean isExtended)
/* Lift up coordinates in .psl file. */
{
FILE *dest = mustOpen(destFile, "w");
char *source;
int i,j;
struct lineFile *lf;
struct psl *psl;
struct xAli *xa = NULL;
unsigned *starts;
unsigned *blockSizes;
struct liftSpec *spec;
int offset;
int blockCount;
char *seqName;
int dotMod = dots;
int seqSize;
int strandChar = (querySide ? 0 : 1);
if (!nohead)
pslWriteHead(dest);
for (i=0; i<sourceCount; ++i)
{
source = sources[i];
if (!fileExists(source))
{
warn("%s doesn't exist!", source);
continue;
}
verbose(1, "Lifting %s\n", source);
lf = pslFileOpenWithMeta(source, dest);
for (;;)
{
if (isExtended)
{
xa = xAliNext(lf);
psl = (struct psl *)xa;
}
else
psl = pslNext(lf);
if (psl == NULL)
break;
boolean isProt = pslIsProtein(psl);
doDots(&dotMod);
if (querySide)
seqName = psl->qName;
else
seqName = psl->tName;
spec = findLift(liftHash, seqName, lf);
if (spec == NULL)
{
if (how != carryMissing)
{
freePslOrXa(psl, isExtended);
continue;
}
}
else
{
offset = spec->offset;
blockSizes = psl->blockSizes;
if (querySide)
{
if (!isPtoG)
{
cantHandleSpecRevStrand(spec);
psl->qStart += offset;
psl->qEnd += offset;
}
else
{
psl->match *= 3;
psl->misMatch *= 3;
if (spec->strand == '-')
{
int tmp = psl->qEnd;
psl->qEnd = psl->qStart;
psl->qStart = tmp;
psl->qStart *= -3;
psl->qEnd *= -3;
psl->qStart += offset;
psl->qEnd += offset;
}
else if (spec->strand == '+')
{
psl->qStart *= 3;
psl->qStart += offset;
psl->qEnd *= 3;
psl->qEnd += offset;
}
}
starts = psl->qStarts;
seqSize = psl->qSize;
}
else
{
if (spec->strand == '-')
reverseIntRange(&psl->tStart, &psl->tEnd, psl->tSize);
psl->tStart += offset;
psl->tEnd += offset;
starts = psl->tStarts;
seqSize = psl->tSize;
}
blockCount = psl->blockCount;
if (isPtoG && (spec->strand == '-'))
{
psl->strand[strandChar] = spec->strand;
for (j=0; j<blockCount; ++j)
{
starts[j] *= -3;
starts[j] += offset;
starts[j] = spec->newSize - starts[j];
}
}
else if (isPtoG && (spec->strand == '+'))
{
psl->strand[strandChar] = spec->strand;
for (j=0; j<blockCount; ++j)
{
starts[j] *= 3;
starts[j] += offset;
}
}
else /* mRNA case. */
{
if (spec->strand == '+')
{
if (psl->strand[strandChar] == '-')
{
for (j=0; j<blockCount; ++j)
{
int tr = seqSize - starts[j];
tr += offset;
starts[j] = spec->newSize - tr;
}
}
else
{
for (j=0; j<blockCount; ++j)
starts[j] += offset;
}
}
else
{
if (isProt)
{
/* if it's protein, we can't reverse the query */
if (psl->strand[strandChar] == '-')
{
for (j=0; j<blockCount; ++j)
starts[j] += offset;
}
else
{
for (j=0; j<blockCount; ++j)
{
int tr = seqSize - starts[j];
tr += offset;
starts[j] = spec->newSize - tr;
}
}
psl->strand[strandChar] =
flipStrand(psl->strand[strandChar]);
}
else
{
if (psl->strand[strandChar] == '-')
errAbort("Can't handle all these minus strands! line %d",lf->lineIx);
else
{
for (j=0; j<blockCount; ++j)
{
psl->tStarts[j] = psl->tSize -
(psl->tStarts[j] + blockSizes[j]) + offset;
psl->qStarts[j] = psl->qSize -
(psl->qStarts[j] + blockSizes[j]); /* no offset. */
}
psl->strand[1-strandChar] =
flipStrand(psl->strand[1-strandChar]);
reverseUnsigned(blockSizes, blockCount);
reverseUnsigned(psl->qStarts, blockCount);
reverseUnsigned(psl->tStarts, blockCount);
}
}
}
}
if (isPtoG)
for (j=0; j<blockCount; ++j)
blockSizes[j] *= 3;
if (querySide)
{
psl->qSize = spec->newSize;
psl->qName = spec->newName;
}
else
{
psl->tSize = spec->newSize;
psl->tName = spec->newName;
}
}
if (isExtended)
{
xAliTabOut(xa, dest);
}
else
{
pslTabOut(psl, dest);
}
if (querySide)
psl->qName = seqName;
else
psl->tName = seqName;
freePslOrXa(psl, isExtended);
}
lineFileClose(&lf);
if (dots)
verbose(1, "\n");
}
if (ferror(dest))
errAbort("error writing %s", destFile);
fclose(dest);
}