static off_t kuSeek(knetFile *fp, int64_t off, int whence)
/* Seek to off according to whence (but don't waste time with samtools' SEEK_END to
* check empty record at end of file. Don't be fooled by the off_t return type --
* it's 0 for OK, non-0 for fail. */
{
bits64 offset;
if (whence == SEEK_SET)
offset = off;
else if (whence == SEEK_CUR)
offset = off+ udcTell(fp->udcf);
else
return -1;
verbose(2, "udcSeek(%lu, %lld)\n", (unsigned long)(fp->udcf), offset);
udcSeek(fp->udcf, offset);
return 0;
}
struct cirTreeFile *cirTreeFileAttach(char *fileName, struct udcFile *udc)
/* Open up r-tree index file on previously open file, with cirTree
* header at current file position. */
{
/* Open file and allocate structure to hold info from header etc. */
struct cirTreeFile *crt = needMem(sizeof(*crt));
crt->fileName = fileName;
crt->udc = udc;
/* Read magic number at head of file and use it to see if we are proper file type, and
* see if we are byte-swapped. */
bits32 magic;
boolean isSwapped = FALSE;
udcMustReadOne(udc, magic);
if (magic != cirTreeSig)
{
magic = byteSwap32(magic);
isSwapped = crt->isSwapped = TRUE;
if (magic != cirTreeSig)
errAbort("%s is not a chromosome id r-tree index file", fileName);
}
/* Read rest of defined bits of header, byte swapping as needed. */
crt->blockSize = udcReadBits32(udc, isSwapped);
crt->itemCount = udcReadBits64(udc, isSwapped);
crt->startChromIx = udcReadBits32(udc, isSwapped);
crt->startBase = udcReadBits32(udc, isSwapped);
crt->endChromIx = udcReadBits32(udc, isSwapped);
crt->endBase = udcReadBits32(udc, isSwapped);
crt->fileSize = udcReadBits64(udc, isSwapped);
crt->itemsPerSlot = udcReadBits32(udc, isSwapped);
/* Skip over reserved bits of header. */
bits32 reserved32;
udcMustReadOne(udc, reserved32);
/* Save position of root block of r tree. */
crt->rootOffset = udcTell(udc);
return crt;
}
struct bptFile *bptFileAttach(char *fileName, struct udcFile *udc)
/* Open up index file on previously open file, with header at current file position. */
{
/* Open file and allocate structure to hold info from header etc. */
struct bptFile *bpt = needMem(sizeof(*bpt));
bpt->fileName = fileName;
bpt->udc = udc;
/* Read magic number at head of file and use it to see if we are proper file type, and
* see if we are byte-swapped. */
bits32 magic;
boolean isSwapped = FALSE;
udcMustReadOne(udc, magic);
if (magic != bptSig)
{
magic = byteSwap32(magic);
isSwapped = bpt->isSwapped = TRUE;
if (magic != bptSig)
errAbort("%s is not a bpt b-plus tree index file", fileName);
}
/* Read rest of defined bits of header, byte swapping as needed. */
bpt->blockSize = udcReadBits32(udc, isSwapped);
bpt->keySize = udcReadBits32(udc, isSwapped);
bpt->valSize = udcReadBits32(udc, isSwapped);
bpt->itemCount = udcReadBits64(udc, isSwapped);
/* Skip over reserved bits of header. */
bits32 reserved32;
udcMustReadOne(udc, reserved32);
udcMustReadOne(udc, reserved32);
/* Save position of root block of b+ tree. */
bpt->rootOffset = udcTell(udc);
return bpt;
}
static void rFindMulti(struct bptFile *bpt, bits64 blockStart, void *key, struct slRef **pList)
/* Find values corresponding to key and add them to pList. You'll need to
* Do a slRefFreeListAndVals() on the list when done. */
{
/* Seek to start of block. */
udcSeek(bpt->udc, blockStart);
/* Read block header. */
UBYTE isLeaf;
UBYTE reserved;
bits16 i, childCount;
udcMustReadOne(bpt->udc, isLeaf);
udcMustReadOne(bpt->udc, reserved);
boolean isSwapped = bpt->isSwapped;
childCount = udcReadBits16(bpt->udc, isSwapped);
int keySize = bpt->keySize;
UBYTE keyBuf[keySize]; /* Place to put a key, buffered on stack. */
UBYTE valBuf[bpt->valSize]; /* Place to put a value, buffered on stack. */
if (isLeaf)
{
for (i=0; i<childCount; ++i)
{
udcMustRead(bpt->udc, keyBuf, keySize);
udcMustRead(bpt->udc, valBuf, bpt->valSize);
if (memcmp(key, keyBuf, keySize) == 0)
{
void *val = cloneMem(valBuf, bpt->valSize);
refAdd(pList, val);
}
}
}
else
{
/* Read first key and first file offset. */
udcMustRead(bpt->udc, keyBuf, keySize);
bits64 lastFileOffset = udcReadBits64(bpt->udc, isSwapped);
bits64 fileOffset = lastFileOffset;
int lastCmp = memcmp(key, keyBuf, keySize);
/* Loop through remainder. */
for (i=1; i<childCount; ++i)
{
udcMustRead(bpt->udc, keyBuf, keySize);
fileOffset = udcReadBits64(bpt->udc, isSwapped);
int cmp = memcmp(key, keyBuf, keySize);
if (lastCmp >= 0 && cmp <= 0)
{
bits64 curPos = udcTell(bpt->udc);
rFindMulti(bpt, lastFileOffset, key, pList);
udcSeek(bpt->udc, curPos);
}
if (cmp < 0)
return;
lastCmp = cmp;
lastFileOffset = fileOffset;
}
/* If made it all the way to end, do last one too. */
rFindMulti(bpt, fileOffset, key, pList);
}
}
static off_t kuTell(knetFile *fp)
/* Tell current offset in file. */
{
verbose(2, "udcTell(%lu)\n", (unsigned long)(fp->udcf));
return udcTell(fp->udcf);
}
