int main(int argc, char *argv[])
/* Process command line. */
{
char *liftFileQ = NULL, *liftFileT = NULL;
optionInit(&argc, argv, optionSpecs);
if (argc != 5)
usage();
tNewR = optionVal("tNewR", tNewR);
qNewR = optionVal("qNewR", qNewR);
noAr = optionExists("noAr");
qRepeatTable = optionVal("qRepeats", qRepeatTable);
tRepeatTable = optionVal("tRepeats", tRepeatTable);
liftFileQ = optionVal("liftQ", liftFileQ);
liftFileT = optionVal("liftT", liftFileT);
if (liftFileQ != NULL)
{
struct liftSpec *lifts = readLifts(liftFileQ);
liftHashQ = hashLift(lifts, TRUE);
}
if (liftFileT != NULL)
{
struct liftSpec *lifts = readLifts(liftFileT);
liftHashT = hashLift(lifts, TRUE);
}
netClass(argv[1], argv[2], argv[3], argv[4]);
return 0;
}
void fixNewLength(char *inFile, char *liftFile, long int size)
{
FILE *liftFh = mustOpen(liftFile, "w");
struct liftSpec *el, *lifts = readLifts(inFile);
for (el = lifts; el != NULL; el = el->next)
{
fprintf(liftFh, "%ld\t%s\t%ld\t%s\t%d\n",el->offset, el->oldName, size, el->newName, el->newSize);
}
carefulClose(&liftFh);
}
int main(int argc, char *argv[])
{
int i;
struct liftSpec *lsList = NULL;
struct hash *liftHash = NULL;
int grouping;
if(argc < 4)
usage();
lsList = readLifts(argv[1]);
liftHash = hashLift(lsList);
grouping = atoi(argv[2]);
for(i=3; i<argc; i++)
affyPairsToSample(liftHash, grouping , argv[i]);
fprintf(stderr,"\nfinished.\n");
return 0;
}
void netContigs(char *netFile, char *liftFile)
/* netContigs - get query-side contigs from a chrom-level net file */
{
struct lineFile *lf = lineFileOpen(netFile, TRUE);
struct chainNet *net;
struct liftSpec *lift, *prevLift, *lifts;
char *chrom;
/* read lift file and split into a hash of per-chrom lists */
lifts = readLifts(liftFile);
prevLift = NULL;
for (lift = lifts; lift != NULL; lift = lift->next)
{
//uglyf("reading lift: %s\n", lift->oldName);
if (hashLookup(chromHash, lift->newName) == NULL)
{
/* new chrom */
//uglyf("adding chrom: %s\n", lift->newName);
hashAdd(chromHash, lift->newName, lift);
/* terminate previous list */
/* NOTE: expects input sorted by chrom */
if (prevLift != NULL)
prevLift->next = NULL;
}
prevLift = lift;
}
/* read in nets and convert query side to contig coords */
//uglyf("reading in nets\n");
while ((net = chainNetRead(lf)) != NULL)
{
rLower(net->fillList);
chainNetFree(&net);
}
/* print accumulated contigs */
hashTraverseEls(contigNames, printContig);
}
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);
}
}
