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;
}
}
struct dnaSeq *nibTwoCacheSeqPartExt(struct nibTwoCache *ntc, char *seqName, int start, int size,
boolean doMask, int *retFullSeqSize)
/* Return part of sequence. If *retFullSeqSize is non-null then return full
* size of sequence (not just loaded part) there. Sequence will be lower
* case if doMask is false, mixed case (repeats in lower)
* if doMask is true. */
{
if (ntc->isTwoBit)
{
return twoBitReadSeqFragExt(ntc->tbf, seqName, start, start+size,
doMask, retFullSeqSize);
}
else
{
struct nibInfo *nib = nibInfoFromCache(ntc->nibHash, ntc->pathName, seqName);
int opts = (doMask ? NIB_MASK_MIXED : 0);
if (retFullSeqSize != NULL)
*retFullSeqSize = nib->size;
return nibLdPartMasked(opts, nib->fileName, nib->f, nib->size, start, size);
}
}
struct dnaSeq *readFromCache(struct dlList *cache, char *dirName, char *seqName,
int start, int size, int seqSize, boolean isTwoBit)
/* Return dnaSeq read from the appropriate nib file.
* You need to dnaSeqFree this when done (it is the nib
* file that is cached, not the sequence). */
{
struct cachedSeqFile *cn = openFromCache(cache, dirName, seqName, isTwoBit);
if (isTwoBit)
{
return twoBitReadSeqFrag(cn->tbf, seqName, start, start+size);
}
else
{
if (seqSize != cn->size)
errAbort("%s/%s is %d bases in .lav file and %d in .nib file\n",
dirName, seqName, seqSize, cn->size);
if ((start+size) > cn->size )
printf("%s/%s is %d bases in .lav file and %d in .nib file start %d size %d end %d\n",
dirName, seqName, seqSize, cn->size, start, size, start+size);
return nibLdPartMasked(NIB_MASK_MIXED, cn->fileName, cn->f, cn->size, start, size);
}
}
struct dnaSeq *nibInfoLoadSeq(struct nibInfo *nib, int start, int size)
/* Load in a sequence in mixed case from nib file. */
{
return nibLdPartMasked(NIB_MASK_MIXED, nib->fileName, nib->f, nib->size,
start, size);
}
