bits32 writeIndexLevel(struct chromInfo **chromArray, int chromCount,
bits32 indexOffset, int level, FILE *f)
/* Write out a non-leaf level. */
{
/* Calculate number of nodes to write at this level. */
int slotSizePer = xToY(blockSize, level); // Number of chroms per slot in node
int nodeSizePer = slotSizePer * blockSize; // Number of chroms per node
int nodeCount = (chromCount + nodeSizePer - 1)/nodeSizePer;
/* Calculate sizes and offsets. */
int bytesInBlock = (2*sizeof(UBYTE) + sizeof(bits16) + blockSize * (2*sizeof(bits32)));
bits32 levelSize = nodeCount * bytesInBlock;
bits32 endLevel = indexOffset + levelSize;
bits32 nextChild = endLevel;
UBYTE isLeaf = FALSE;
UBYTE reserved = 0;
int i,j;
for (i=0; i<chromCount; i += nodeSizePer)
{
/* Calculate size of this block */
bits16 countOne = (chromCount - i + slotSizePer - 1)/slotSizePer;
if (countOne > blockSize)
countOne = blockSize;
/* Write block header. */
writeOne(f, isLeaf);
writeOne(f, reserved);
writeOne(f, countOne);
int slotsUsed = 0;
int endIx = i + nodeSizePer;
if (endIx > chromCount)
endIx = chromCount;
for (j=i; j<endIx; j += slotSizePer)
{
struct chromInfo *chrom = chromArray[j];
writeOne(f, chrom->genomeOffset);
writeOne(f, nextChild);
nextChild += bytesInBlock;
++slotsUsed;
}
assert(slotsUsed == countOne);
for (j=countOne; j<blockSize; ++j)
{
bits32 genomeOffsetPad=0;
bits32 binFileOffsetPad=0;
writeOne(f, genomeOffsetPad);
writeOne(f, binFileOffsetPad);
}
}
return endLevel;
}
static bits32 writeIndexLevel(bits16 blockSize,
void *itemArray, int itemSize, long itemCount,
bits32 indexOffset, int level,
void (*fetchKey)(const void *va, char *keyBuf), bits32 keySize, bits32 valSize,
FILE *f)
/* Write out a non-leaf level. */
{
char *items = itemArray;
/* Calculate number of nodes to write at this level. */
long slotSizePer = xToY(blockSize, level); // Number of items per slot in node
long nodeSizePer = slotSizePer * blockSize; // Number of items per node
long nodeCount = (itemCount + nodeSizePer - 1)/nodeSizePer;
/* Calculate sizes and offsets. */
long bytesInIndexBlock = (bptBlockHeaderSize + blockSize * (keySize+sizeof(bits64)));
long bytesInLeafBlock = (bptBlockHeaderSize + blockSize * (keySize+valSize));
bits64 bytesInNextLevelBlock = (level == 1 ? bytesInLeafBlock : bytesInIndexBlock);
bits64 levelSize = nodeCount * bytesInIndexBlock;
bits64 endLevel = indexOffset + levelSize;
bits64 nextChild = endLevel;
UBYTE isLeaf = FALSE;
UBYTE reserved = 0;
long i,j;
char keyBuf[keySize+1];
keyBuf[keySize] = 0;
for (i=0; i<itemCount; i += nodeSizePer)
{
/* Calculate size of this block */
long countOne = (itemCount - i + slotSizePer - 1)/slotSizePer;
if (countOne > blockSize)
countOne = blockSize;
bits16 shortCountOne = countOne;
/* Write block header. */
writeOne(f, isLeaf);
writeOne(f, reserved);
writeOne(f, shortCountOne);
/* Write out the slots that are used one by one, and do sanity check. */
int slotsUsed = 0;
long endIx = i + nodeSizePer;
if (endIx > itemCount)
endIx = itemCount;
for (j=i; j<endIx; j += slotSizePer)
{
void *item = items + j*itemSize;
memset(keyBuf, 0, keySize);
(*fetchKey)(item, keyBuf);
mustWrite(f, keyBuf, keySize);
writeOne(f, nextChild);
nextChild += bytesInNextLevelBlock;
++slotsUsed;
}
assert(slotsUsed == shortCountOne);
/* Write out empty slots as all zero. */
int slotSize = keySize + sizeof(bits64);
for (j=countOne; j<blockSize; ++j)
repeatCharOut(f, 0, slotSize);
}
return endLevel;
}
