void maskWithOut(char *outName, struct hash *tbHash, struct hash *bitmapHash)
/* Read coordinates from outName and apply them to twoBits in tbHash. */
{
struct lineFile *lf = lineFileOpen(outName, TRUE);
char *line;
int lineSize;
/* Make sure we have a .out header. */
if (!lineFileNext(lf, &line, &lineSize))
errAbort("Empty %s", lf->fileName);
if (!startsWith(" SW perc perc", line))
{
if (!startsWith(" SW perc perc", line))
errAbort("%s doesn't seem to be a RepeatMasker .out file, first "
"line seen:\n%s", lf->fileName, line);
}
lineFileNext(lf, &line, &lineSize);
lineFileNext(lf, &line, &lineSize);
/* Process line oriented records of .out file. */
while (lineFileNext(lf, &line, &lineSize))
{
struct repeatMaskOut rmo;
char *words[24];
int wordCount;
char *seqName;
int start, end;
wordCount = chopLine(line, words);
if (wordCount < 14)
errAbort("Expecting 14 or 15 words line %d of %s",
lf->lineIx, lf->fileName);
repeatMaskOutStaticLoad(words, &rmo);
seqName = rmo.qName;
start = rmo.qStart - 1;
end = rmo.qEnd;
addMasking(tbHash, bitmapHash, seqName, start, end);
}
bitmapToMaskArray(bitmapHash, tbHash);
}
void storeMasked(struct hash *repeatHash, char *faName)
/* Look for repeat masked file corresponding to faName. */
{
char fileName[512];
struct lineFile *lf;
char *line;
int lineSize;
struct repeatMaskOut rmo;
struct hashEl *hel;
struct repeatTracker *rt;
boolean ok;
sprintf(fileName, "%s.out", faName);
if (!fileExists(fileName))
{
warn("No mask file %s\n", fileName);
return;
}
lf = lineFileOpen(fileName, TRUE);
ok = lineFileNext(lf, &line, &lineSize);
if (!ok)
warn("Empty mask file %s\n", fileName);
else
{
if (!startsWith("There were no", line))
{
if (!startsWith(" SW", line))
errAbort("%s isn't a RepeatMasker .out file.", fileName);
if (!lineFileNext(lf, &line, &lineSize) || !startsWith("score", line))
errAbort("%s isn't a RepeatMasker .out file.", fileName);
lineFileNext(lf, &line, &lineSize); /* Blank line. */
while (lineFileNext(lf, &line, &lineSize))
{
char *words[32];
int wordCount;
int seqSize;
int repSize;
wordCount = chopLine(line, words);
if (wordCount < 14)
errAbort("%s line %d - error in repeat mask .out file\n", fileName, lf->lineIx);
repeatMaskOutStaticLoad(words, &rmo);
/* If repeat is more than 15% divergent don't worry about it. */
if (rmo.percDiv + rmo.percDel + rmo.percInc <= 15.0)
{
if ((hel = hashLookup(repeatHash, rmo.qName)) == NULL)
errAbort("%s is in %s but not %s, files out of sync?\n", rmo.qName, fileName, faName);
rt = hel->val;
seqSize = rt->seq->size;
if (rmo.qStart <= 0 || rmo.qStart > seqSize || rmo.qEnd <= 0 || rmo.qEnd > seqSize || rmo.qStart > rmo.qEnd)
{
warn("Repeat mask sequence out of range (%d-%d of %d in %s)\n",
rmo.qStart, rmo.qEnd, seqSize, rmo.qName);
if (rmo.qStart <= 0)
rmo.qStart = 1;
if (rmo.qEnd > seqSize)
rmo.qEnd = seqSize;
}
repSize = rmo.qEnd - rmo.qStart + 1;
if (repSize > 0)
memset(rt->repBytes + rmo.qStart - 1, TRUE, repSize);
}
}
}
}
lineFileClose(&lf);
}
