void netLineFilter(struct lineFile *lf, FILE *f)
/* Do filter one line at a time. */
{
struct hash *nameHash = newHash(0);
char *line, *l;
int d;
while (lineFileNext(lf, &line, NULL))
{
d = countLeadingChars(line, ' ');
l = line + d;
if (startsWith("fill", l) || startsWith("gap", l))
{
struct cnFill *fill = cnFillFromLine(nameHash, lf, l);
if (filterOne(fill))
cnFillWrite(fill, f, d);
cnFillFree(&fill);
}
else
{
fprintf(f, "%s\n", line);
}
}
hashFree(&nameHash);
}
void cnFillWrite(struct cnFill *fillList, FILE *f, int depth)
/* Recursively write out fill list. */
{
struct cnFill *fill;
for (fill = fillList; fill != NULL; fill = fill->next)
{
char *type = (fill->chainId ? "fill" : "gap");
spaceOut(f, depth);
fprintf(f, "%s %d %d %s %c %d %d", type, fill->tStart, fill->tSize,
fill->qName, fill->qStrand, fill->qStart, fill->qSize);
if (fill->chainId)
fprintf(f, " id %d", fill->chainId);
if (fill->score > 0)
fprintf(f, " score %1.0f", fill->score);
if (fill->ali > 0)
fprintf(f, " ali %d", fill->ali);
if (fill->qOver >= 0)
fprintf(f, " qOver %d", fill->qOver);
if (fill->qFar >= 0)
fprintf(f, " qFar %d", fill->qFar);
if (fill->qDup >= 0)
fprintf(f, " qDup %d", fill->qDup);
if (fill->type != NULL)
fprintf(f, " type %s", fill->type);
if (fill->tN >= 0)
fprintf(f, " tN %d", fill->tN);
if (fill->qN >= 0)
fprintf(f, " qN %d", fill->qN);
if (fill->tR >= 0)
fprintf(f, " tR %d", fill->tR);
if (fill->qR >= 0)
fprintf(f, " qR %d", fill->qR);
if (fill->tNewR >= 0)
fprintf(f, " tNewR %d", fill->tNewR);
if (fill->qNewR >= 0)
fprintf(f, " qNewR %d", fill->qNewR);
if (fill->tOldR >= 0)
fprintf(f, " tOldR %d", fill->tOldR);
if (fill->qOldR >= 0)
fprintf(f, " qOldR %d", fill->qOldR);
if (fill->tTrf >= 0)
fprintf(f, " tTrf %d", fill->tTrf);
if (fill->qTrf >= 0)
fprintf(f, " qTrf %d", fill->qTrf);
fputc('\n', f);
if (fill->children)
cnFillWrite(fill->children, f, depth+1);
}
}
void chainNetWrite(struct chainNet *net, FILE *f)
/* Write out chain net. */
{
fprintf(f, "net %s %d\n", net->name, net->size);
cnFillWrite(net->fillList, f, 1);
}
