bits32 bbiChromSize(struct bbiFile *bbi, char *chrom)
/* Return chromosome size, or 0 if no such chromosome in file. */
{
struct bbiChromIdSize idSize;
if (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize)))
return 0;
return idSize.chromSize;
}
static int bbiChromId(struct bbiFile *bbi, char *chrom)
/* Return chromosome size */
{
struct bbiChromIdSize idSize;
if (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize)))
return -1;
return idSize.chromId;
}
void bptLookupStringToBits64(char *indexFile, char *string)
/* bptLookupStringToBits64 - Given a string value look up and return associated 64 bit value if
* any */
{
struct bptFile *bpt = bptFileOpen(indexFile);
bits64 val;
if (bptFileFind(bpt, string, strlen(string), &val, sizeof(val)) )
printf("%lld\n", val);
else
errAbort("%s not found", string);
}
struct fileOffsetSize *crTreeFindOverlappingBlocks(struct crTreeFile *crt,
char *chrom, bits32 start, bits32 end)
/* Return list of file blocks that between them contain all items that overlap
* start/end on chromIx. Also there will be likely some non-overlapping items
* in these blocks too. When done, use slListFree to dispose of the result. */
{
/* Find chromosome index. Return NULL if no such chromosome*/
bits32 chromIx;
if (!bptFileFind(crt->chromBpt, chrom, strlen(chrom), &chromIx, sizeof(chromIx)))
return NULL;
return cirTreeFindOverlappingBlocks(crt->cir, chromIx, start, end);
}
struct fileOffsetSize *bbiOverlappingBlocks(struct bbiFile *bbi, struct cirTreeFile *ctf,
char *chrom, bits32 start, bits32 end, bits32 *retChromId)
/* Fetch list of file blocks that contain items overlapping chromosome range. */
{
struct bbiChromIdSize idSize;
if (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize)))
return NULL;
if (bbi->isSwapped)
idSize.chromId = byteSwap32(idSize.chromId);
if (retChromId != NULL)
*retChromId = idSize.chromId;
return cirTreeFindOverlappingBlocks(ctf, idSize.chromId, start, end);
}
