void writeFiltered(struct chainNet *net, FILE *f)
/* Write out parts of net that pass filter to file. */
{
if ((net->fillList = cnPrune(net->fillList)) != NULL)
{
chainNetWrite(net, f);
}
}
void liftNet(char *destFile, struct hash *liftHash,
int sourceCount, char *sources[], boolean querySide)
/* Lift up coordinates in .net file. */
{
FILE *f = mustOpen(destFile, "w");
int sourceIx;
int dotMod = dots;
for (sourceIx = 0; sourceIx < sourceCount; ++sourceIx)
{
char *source = sources[sourceIx];
struct lineFile *lf = lineFileOpen(source, TRUE);
struct chainNet *net;
lineFileSetMetaDataOutput(lf, f);
verbose(1, "Lifting %s\n", source);
while ((net = chainNetRead(lf)) != NULL)
{
if (querySide)
{
struct hash *newNameHash = hashNew(6);
liftFillsQ(net->fillList, newNameHash, liftHash, lf);
hashFree(&(net->nameHash));
net->nameHash = newNameHash;
}
else
{
struct liftSpec *spec = findLift(liftHash, net->name, lf);
if (spec == NULL)
{
if (how != carryMissing)
{
chainNetFree(&net);
continue;
}
}
else
{
freeMem(net->name);
net->name = cloneString(spec->newName);
net->size = spec->newSize;
liftFillsT(net->fillList, spec);
}
}
chainNetWrite(net, f);
chainNetFree(&net);
doDots(&dotMod);
}
lineFileClose(&lf);
if (dots)
verbose(1, "\n");
}
}
void netClass(char *inName, char *tDb, char *qDb, char *outName)
/* netClass - Add classification info to net. */
{
struct chainNet *net;
struct lineFile *lf = lineFileOpen(inName, TRUE);
FILE *f = mustOpen(outName, "w");
struct chrom *qChromList, *chrom;
struct hash *qChromHash;
struct hash *arHash = NULL;
struct sqlConnection *tConn = sqlConnect(tDb);
struct sqlConnection *qConn = sqlConnect(qDb);
qLm = lmInit(0);
if (!noAr)
arHash = getAncientRepeats(tConn, qConn);
getChroms(qConn, &qChromHash, &qChromList);
verbose(1, "Reading gaps in %s\n", qDb);
if (sqlTableExists(qConn, "gap"))
{
getSeqGapsUnsplit(qConn, qChromHash);
}
else
{
for (chrom = qChromList; chrom != NULL; chrom = chrom->next)
chrom->nGaps = getSeqGaps(qConn, chrom->name);
}
if (qNewR)
{
verbose(1, "Reading new repeats from %s\n", qNewR);
for (chrom = qChromList; chrom != NULL; chrom = chrom->next)
chrom->newRepeats = getNewRepeats(qNewR, chrom->name);
}
verbose(1, "Reading simpleRepeats in %s\n", qDb);
getTrfUnsplit(qConn, qChromHash);
if (qRepeatTable)
{
verbose(1, "Reading repeats in %s from table %s\n", qDb, qRepeatTable);
getRepeatsUnsplitTable(qConn, qChromHash, qRepeatTable);
}
else
{
verbose(1, "Reading repeats in %s\n", qDb);
if (sqlTableExists(qConn, "rmsk"))
getRepeatsUnsplit(qConn, qChromHash, arHash);
else
{
for (chrom = qChromList; chrom != NULL; chrom = chrom->next)
getRepeats(qConn, arHash, chrom->name, &chrom->repeats,
&chrom->oldRepeats);
}
}
while ((net = chainNetRead(lf)) != NULL)
{
struct rbTree *tN, *tRepeats, *tOldRepeats, *tTrf;
char *tName = net->name;
if (liftHashT != NULL)
{
struct liftSpec *lft = hashMustFindVal(liftHashT, net->name);
tName = lft->newName;
}
verbose(1, "Processing %s.%s\n", tDb, net->name);
tN = getSeqGaps(tConn, tName);
tAddN(net, net->fillList, tN);
rbTreeFree(&tN);
qAddN(net, net->fillList, qChromHash);
if (tRepeatTable)
getRepeatsTable(tConn, tRepeatTable, tName, &tRepeats, &tOldRepeats);
else
getRepeats(tConn, arHash, tName, &tRepeats, &tOldRepeats);
tAddR(net, net->fillList, tRepeats);
if (!noAr)
tAddOldR(net, net->fillList, tOldRepeats);
rbTreeFree(&tRepeats);
rbTreeFree(&tOldRepeats);
qAddR(net, net->fillList, qChromHash);
if (!noAr)
qAddOldR(net, net->fillList, qChromHash);
tTrf = getTrf(tConn, tName);
tAddTrf(net, net->fillList, tTrf);
rbTreeFree(&tTrf);
qAddTrf(net, net->fillList, qChromHash);
if (tNewR)
{
struct rbTree *tree = getNewRepeats(tNewR, tName);
tAddNewR(net, net->fillList, tree);
rbTreeFree(&tree);
}
if (qNewR)
qAddNewR(net, net->fillList, qChromHash);
chainNetWrite(net, f);
chainNetFree(&net);
}
sqlDisconnect(&tConn);
sqlDisconnect(&qConn);
}
