struct dnaSeq *dnaLoadSingle(char *fileName, int *retStart, int *retEnd, int *retParentSize)
/* Return sequence if it's a nib file or 2bit part, NULL otherwise. */
{
struct dnaSeq *seq = NULL;
unsigned start = 0, end = 0;
int parentSize = 0;
if (nibIsFile(fileName))
{
/* Save offset out of fileName for auto-lifting */
char filePath[PATH_LEN];
char name[PATH_LEN];
nibParseName(0, fileName, filePath, name, &start, &end);
if (end != 0) /* It's just a range. */
{
FILE *f;
int size;
nibOpenVerify(filePath, &f, &size);
parentSize = size;
}
seq = nibLoadAllMasked(NIB_MASK_MIXED, fileName);
if (end == 0)
parentSize = end = seq->size;
freez(&seq->name);
seq->name = cloneString(name);
}
else if (twoBitIsRange(fileName))
{
/* Save offset out of fileName for auto-lifting */
char *rangeSpec = cloneString(fileName);
int start, end;
char *file, *seqName;
twoBitParseRange(rangeSpec, &file, &seqName, &start, &end);
/* Load sequence. */
{
struct twoBitFile *tbf = twoBitOpen(file);
parentSize = twoBitSeqSize(tbf, seqName);
seq = twoBitReadSeqFrag(tbf, seqName, start, end);
twoBitClose(&tbf);
}
if (end == 0)
end = seq->size;
freez(&rangeSpec);
}
if (retStart != NULL)
*retStart = start;
if (retEnd != NULL)
*retEnd = end;
if (retParentSize != NULL)
*retParentSize = parentSize;
return seq;
}
void twoBitInfo(char *inName, char *outName)
/* twoBitInfo - get information about sequences in a .2bit file. */
{
struct twoBitFile *tbf;
FILE *outFile;
char *seqName = NULL;
twoBitParseRange(inName, &inName, &seqName, NULL, NULL);
tbf = twoBitOpen(inName);
outFile = mustOpen(outName, "w");
if (seqName != NULL)
{
char *seqArray[1023];
int i;
int seqCount = chopString(seqName, ",", seqArray, ArraySize(seqArray));
for (i = 0 ; i < seqCount ; i++)
{
if (optionExists("maskBed"))
twoBitOutMaskBeds(tbf, seqArray[i], outFile);
else if (optionExists("nBed"))
twoBitOutNBeds(tbf, seqArray[i], outFile);
else if(optionExists("noNs"))
fprintf(outFile, "%s\t%d\n", seqArray[i], twoBitSeqSizeNoNs(tbf, seqArray[i]));
else
fprintf(outFile, "%s\t%d\n", seqArray[i], twoBitSeqSize(tbf, seqArray[i]));
}
}
else
{
struct twoBitIndex *index;
for (index = tbf->indexList; index != NULL; index = index->next)
{
if (optionExists("maskBed"))
twoBitOutMaskBeds(tbf, index->name, outFile);
else if (optionExists("nBed"))
twoBitOutNBeds(tbf, index->name, outFile);
else if(optionExists("noNs"))
fprintf(outFile, "%s\t%d\n", index->name, twoBitSeqSizeNoNs(tbf, index->name));
else
fprintf(outFile, "%s\t%d\n", index->name, twoBitSeqSize(tbf, index->name));
}
}
twoBitClose(&tbf);
carefulClose(&outFile);
}
