void readCachedSeqPart(char *seqName, int start, int size, boolean getMasked,
struct hash *hash, struct dlList *fileCache,
struct dnaSeq **retSeq, int *retOffset, boolean *retIsNib)
/* Read sequence hopefully using file cashe. If sequence is in a nib
* file just read part of it. */
{
struct seqFilePos *sfp = hashMustFindVal(hash, seqName);
FILE *f = openFromCache(fileCache, sfp);
if (sfp->isTwoBit)
{
*retSeq = twoBitReadSeqFrag((struct twoBitFile *)f, seqName, start, start + size);
*retOffset = start;
*retIsNib = TRUE;
}
else if (sfp->isNib)
{
*retSeq = nibLdPartMasked((getMasked ? NIB_MASK_MIXED : 0), sfp->file, f, sfp->pos, start, size);
*retOffset = start;
*retIsNib = TRUE;
}
else
{
if (getMasked)
errAbort("masked sequences not supported with fasta files");
*retSeq = readSeqFromFaPos(sfp, f);
*retOffset = 0;
*retIsNib = FALSE;
}
}
void readCachedSeqPart(char *seqName, int start, int size,
struct hash *hash, struct dlList *fileCache,
struct dnaSeq **retSeq, int *retOffset, boolean *retIsPartial)
/* Read sequence hopefully using file cashe. If sequence is in a nib
* file just read part of it. */
{
struct seqFilePos *sfp = hashMustFindVal(hash, seqName);
FILE *f = openFromCache(fileCache, sfp->file);
if (sfp->isNib)
{
*retSeq = nibLdPartMasked(NIB_MASK_MIXED, sfp->file, f, sfp->pos, start, size);
*retOffset = start;
*retIsPartial = TRUE;
}
else if (sfp->isTwoBit)
{
*retSeq = twoBitReadSeqFrag(sfp->tbf, seqName, start, start+size);
*retOffset = start;
*retIsPartial = TRUE;
}
else
{
*retSeq = readSeqFromFaPos(sfp, f);
*retOffset = 0;
*retIsPartial = FALSE;
}
}
