void rmskOutWriteAllOut(char *fileName, struct rmskOut *rmskList)
/* Write .out format file containing all in rmskList. */
{
FILE *f = mustOpen(fileName, "w");
struct rmskOut *rmsk;
rmskOutWriteHead(f);
for (rmsk = rmskList; rmsk != NULL; rmsk = rmsk->next)
rmskOutWriteOneOut(rmsk, f);
fclose(f);
}
void liftOut(char *destFile, struct hash *liftHash, int sourceCount, char *sources[])
/* Lift up coordinates in .out file. Add offset to id (15th) column to
* maintain non-overlapping id ranges for different input files. */
{
FILE *dest = mustOpen(destFile, "w");
char *source;
int i;
struct lineFile *lf;
int lineSize, wordCount;
char *line, *words[32];
char *s;
int begin, end, left;
char leftString[18];
int highestIdSoFar = 0, idOffset = 0;
char idStr[32];
struct liftSpec *spec;
char *newName;
rmskOutWriteHead(dest);
for (i=0; i<sourceCount; ++i)
{
source = sources[i];
verbose(1, "Lifting %s\n", source);
if (!fileExists(source))
{
warn("%s does not exist\n", source);
continue;
}
lf = lineFileOpen(source, TRUE);
if (!lineFileNext(lf, &line, &lineSize))
{
warn("%s is empty\n", source);
lineFileClose(&lf);
continue;
}
if (startsWith("There were no", line))
{
lineFileClose(&lf);
continue;
}
skipLines(lf, 2);
while (lineFileNext(lf, &line, &lineSize))
{
wordCount = chopLine(line, words);
// 16 becomes 17, new field in RMasker June23 '03 - Hiram
if (wordCount < 14 || wordCount > 17)
errAbort("Expecting 14-17 words (found %d) line %d of %s", wordCount, lf->lineIx, lf->fileName);
if (wordCount >= 15)
{
if (words[14][0] == '*')
{
warn("Warning: 15th column has * (should be a numeric ID).\n");
idStr[0] = '\0';
}
else
{
int numId = sqlUnsigned(words[14]) + idOffset;
if (numId > highestIdSoFar)
highestIdSoFar = numId;
safef(idStr, sizeof(idStr), "%d", numId);
}
}
else
idStr[0] = '\0';
begin = numField(words, 5, 0, lf);
end = numField(words, 6, 0, lf);
s = words[7];
if (s[0] != '(')
errAbort("Expecting parenthesized field 8 line %d of %s", lf->lineIx, lf->fileName);
left = numField(words, 7, 1, lf);
spec = findLift(liftHash, words[4], lf);
if (spec == NULL)
{
if (how == carryMissing)
newName = words[4];
else
continue;
}
else
{
cantHandleSpecRevStrand(spec);
begin += spec->offset;
end += spec->offset;
left = spec->newSize - end;
newName = spec->newName;
}
sprintf(leftString, "(%d)", left);
fprintf(dest,
"%5s %5s %4s %4s %-9s %7d %7d %9s %1s %-14s %-19s %6s %4s %6s %6s\n",
words[0], words[1], words[2], words[3], newName,
begin, end, leftString,
words[8], words[9], words[10], words[11], words[12], words[13], idStr);
}
lineFileClose(&lf);
idOffset = highestIdSoFar;
}
if (ferror(dest))
errAbort("error writing %s", destFile);
fclose(dest);
}
