void liftAcross(char *liftAcross, char *srcFile, char *dstOut)
/* liftAcross - convert one coordinate system to another, no overlapping items. */
{
struct hash *lftHash = readLift(liftAcross);
struct genePred *gpList = genePredExtLoadAll(srcFile);
struct genePred *gp = NULL;
FILE *out = mustOpen(dstOut, "w");
if (bedOut)
bedRegionOutput(lftHash);
int genePredItemCount = 0;
for (gp = gpList; gp != NULL; gp = gp->next)
{
struct liftSpec *lsFound = hashFindVal(lftHash, gp->chrom);
if (lsFound)
{
struct genePred *gpLifted = liftGenePred(gp, lsFound);
struct genePred *gpl;
for (gpl = gpLifted; gpl != NULL; gpl = gpl->next)
genePredTabOut(gpl, out);
genePredFreeList(&gpLifted);
}
else
{
genePredTabOut(gp, out);
}
++genePredItemCount;
}
/* lftHash and gpList are left allocated to disappear at exit */
verbose(2,"#\tgene pred item count: %d\n", genePredItemCount);
}
void liftUp(char *destFile, char *liftFile, char *howSpec, int sourceCount, char *sources[])
/* liftUp - change coordinates of .psl, .agp, or .out file
* to parent coordinate system. */
{
struct liftSpec *lifts = NULL;
struct hash *liftHash;
char *destType = optionVal("type", destFile);
if (sameWord(howSpec, "carry"))
how = carryMissing;
else if (sameWord(howSpec, "warn"))
how = warnMissing;
else if (sameWord(howSpec, "drop"))
how = silentDrop;
else if (sameWord(howSpec, "error"))
how = errorMissing;
else
usage();
if (how == carryMissing && sameString("/dev/null", liftFile))
verbose(1, "Carrying input -- ignoring /dev/null liftFile\n");
else
{
lifts = readLifts(liftFile);
verbose(1, "Got %d lifts in %s\n", slCount(lifts), liftFile);
}
if (endsWith(destType, ".out"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, FALSE);
liftOut(destFile, liftHash, sourceCount, sources);
}
else if (endsWith(destType, ".pslx") || endsWith(destType, ".xa") || endsWith(destType, ".psl"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, TRUE);
liftPsl(destFile, liftHash, sourceCount, sources,
optionExists("pslQ") || optionExists("pslq"), !endsWith(destType, ".psl") );
}
else if (endsWith(destType, ".agp"))
{
liftHash = hashLift(lifts, FALSE);
liftAgp(destFile, liftHash, sourceCount, sources);
}
else if (endsWith(destType, ".gap"))
{
liftHash = hashLift(lifts, TRUE);
liftGap(destFile, liftHash, sourceCount, sources);
}
else if (endsWith(destType, ".gl"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, FALSE);
liftGl(destFile, liftHash, sourceCount, sources);
}
else if (endsWith(destType, ".gff") || endsWith(destType, ".gtf"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, TRUE);
liftGff(destFile, liftHash, sourceCount, sources);
}
else if (endsWith(destType, ".gdup"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, FALSE);
liftGdup(destFile, liftHash, sourceCount, sources);
}
else if (endsWith(destType, ".bed"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, TRUE);
liftBed(destFile, liftHash, sourceCount, sources);
}
else if (endsWith(destType, ".bed8"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, TRUE);
liftBed8(destFile, liftHash, sourceCount, sources);
}
else if (endsWith(destType, ".gp") || endsWith(destType, ".genepred"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, TRUE);
if (extGenePred)
liftGenePredExt(destFile, liftHash, sourceCount, sources);
else
liftGenePred(destFile, liftHash, sourceCount, sources);
}
else if (endsWith(destType, ".bscore"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, TRUE);
liftBScore(destFile, liftHash, sourceCount, sources,
optionExists("pslQ") || optionExists("pslq"));
}
else if (endsWith(destType, ".tab"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, TRUE);
liftBlast(destFile, liftHash, sourceCount, sources);
}
else if (strstr(destType, "gold"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, FALSE);
liftAgp(destFile, liftHash, sourceCount, sources);
}
else if (strstr(destType, ".axt"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, FALSE);
liftAxt(destFile, liftHash, sourceCount, sources,
optionExists("axtQ") || optionExists("axtq"));
}
else if (strstr(destType, ".chain"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, TRUE);
liftChain(destFile, liftHash, sourceCount, sources,
optionExists("chainQ") || optionExists("chainq"));
}
else if (strstr(destType, ".net"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, FALSE);
liftNet(destFile, liftHash, sourceCount, sources,
optionExists("netQ") || optionExists("netq"));
}
else if (strstr(destType, ".wab"))
{
rmChromPart(lifts);
liftHash = hashLift(lifts, FALSE);
liftWab(destFile, liftHash, sourceCount, sources,
optionExists("wabaQ") || optionExists("wabaq"));
}
else
{
errAbort("Unknown file suffix for %s\n", destType);
}
}
