static boolean rFind(struct bptFile *bpt, bits64 blockStart, void *key, void *val)
/* Find value corresponding to key. If found copy value to memory pointed to by val and return
* true. Otherwise return false. */
{
/* 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);
UBYTE keyBuf[bpt->keySize]; /* Place to put a key, buffered on stack. */
if (isLeaf)
{
for (i=0; i<childCount; ++i)
{
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
udcMustRead(bpt->udc, val, bpt->valSize);
if (memcmp(key, keyBuf, bpt->keySize) == 0)
return TRUE;
}
return FALSE;
}
else
{
/* Read and discard first key. */
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
/* Scan info for first file offset. */
bits64 fileOffset = udcReadBits64(bpt->udc, isSwapped);
/* Loop through remainder. */
for (i=1; i<childCount; ++i)
{
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
if (memcmp(key, keyBuf, bpt->keySize) < 0)
break;
fileOffset = udcReadBits64(bpt->udc, isSwapped);
}
return rFind(bpt, fileOffset, key, val);
}
}
static bits64 bptDataStart(struct bptFile *bpt)
/* Return offset of first bit of data (as opposed to index) in file. In hind sight I wish
* this were stored in the header, but fortunately it's not that hard to compute. */
{
bits64 offset = bpt->rootOffset;
for (;;)
{
/* Seek to block start */
udcSeek(bpt->udc, offset);
/* Read block header, break if we are leaf. */
UBYTE isLeaf;
UBYTE reserved;
bits16 childCount;
udcMustReadOne(bpt->udc, isLeaf);
if (isLeaf)
break;
udcMustReadOne(bpt->udc, reserved);
boolean isSwapped = bpt->isSwapped;
childCount = udcReadBits16(bpt->udc, isSwapped);
/* Read and discard first key. */
char keyBuf[bpt->keySize];
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
/* Get file offset of sub-block. */
offset = udcReadBits64(bpt->udc, isSwapped);
}
return offset;
}
struct bptFile *bigBedOpenExtraIndex(struct bbiFile *bbi, char *fieldName, int *retFieldIx)
/* Return index associated with fieldName. Aborts if no such index. Optionally return
* index in a row of this field. */
{
struct udcFile *udc = bbi->udc;
boolean isSwapped = bbi->isSwapped;
struct asObject *as = bigBedAsOrDefault(bbi);
struct asColumn *col = asColumnFind(as, fieldName);
if (col == NULL)
errAbort("No field %s in %s", fieldName, bbi->fileName);
int colIx = slIxFromElement(as->columnList, col);
if (retFieldIx != NULL)
*retFieldIx = colIx;
asObjectFree(&as);
/* See if we have any extra indexes, and if so seek to there. */
bits64 offset = bbi->extraIndexListOffset;
if (offset == 0)
errAbort("%s has no indexes", bbi->fileName);
udcSeek(udc, offset);
/* Go through each extra index and see if it's a match */
int i;
for (i=0; i<bbi->extraIndexCount; ++i)
{
bits16 type = udcReadBits16(udc, isSwapped);
bits16 fieldCount = udcReadBits16(udc, isSwapped);
bits64 fileOffset = udcReadBits64(udc, isSwapped);
udcSeekCur(udc, 4); // skip over reserved bits
if (type != 0)
{
warn("Don't understand type %d", type);
internalErr();
}
if (fieldCount == 1)
{
bits16 fieldId = udcReadBits16(udc, isSwapped);
udcSeekCur(udc, 2); // skip over reserved bits
if (fieldId == colIx)
{
udcSeek(udc, fileOffset);
struct bptFile *bpt = bptFileAttach(bbi->fileName, udc);
return bpt;
}
}
else
{
warn("Not yet understanding indexes on multiple fields at once.");
internalErr();
}
}
errAbort("%s is not indexed in %s", fieldName, bbi->fileName);
return NULL;
}
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 crTreeFile *crTreeFileOpen(char *fileName)
/* Open up r-tree index file - reading headers and verifying things. */
{
/* Open file and allocate structure to hold info from header etc. */
struct udcFile *udc = udcFileOpen(fileName, udcDefaultDir());
struct crTreeFile *crt = needMem(sizeof(*crt));
fileName = crt->fileName = cloneString(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 != crTreeSig)
{
magic = byteSwap32(magic);
isSwapped = crt->isSwapped = TRUE;
if (magic != crTreeSig)
errAbort("%s is not a chromosome r-tree index file", fileName);
}
/* Read rest of high level header including notably the offsets to the
* chromosome and range indexes. */
bits32 reserved32;
udcMustReadOne(udc, reserved32);
crt->chromOffset = udcReadBits64(udc, isSwapped);
crt->cirOffset = udcReadBits64(udc, isSwapped);
/* Read in the chromosome index header. */
udcSeek(udc, crt->chromOffset);
crt->chromBpt = bptFileAttach(fileName, udc);
/* Read in range index header. */
udcSeek(udc, crt->cirOffset);
crt->cir = cirTreeFileAttach(fileName, udc);
return crt;
}
static void rTraverse(struct bptFile *bpt, bits64 blockStart, void *context,
void (*callback)(void *context, void *key, int keySize, void *val, int valSize) )
/* Recursively go across tree, calling callback at leaves. */
{
/* 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);
char keyBuf[bpt->keySize], valBuf[bpt->valSize];
if (isLeaf)
{
for (i=0; i<childCount; ++i)
{
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
udcMustRead(bpt->udc, valBuf, bpt->valSize);
callback(context, keyBuf, bpt->keySize, valBuf, bpt->valSize);
}
}
else
{
bits64 fileOffsets[childCount];
/* Loop through to get file offsets of children. */
for (i=0; i<childCount; ++i)
{
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
fileOffsets[i] = udcReadBits64(bpt->udc, isSwapped);
}
/* Loop through recursing on child offsets. */
for (i=0; i<childCount; ++i)
rTraverse(bpt, fileOffsets[i], context, callback);
}
}
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);
}
}
struct bbiFile *bbiFileOpenWithDir(char *fileName, bits32 sig, char *typeName, char *udcDir)
/* same (mostly) as bbiFileOpen in bbiFile.c, but allows setting the temporary dir */
{
struct bbiFile *bbi;
AllocVar(bbi);
bbi->fileName = cloneString(fileName);
struct udcFile *udc = bbi->udc = udcFileOpen(fileName, udcDir);
/* 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;
udcMustRead(udc, &magic, sizeof(magic));
if (magic != sig)
{
magic = byteSwap32(magic);
isSwapped = TRUE;
if (magic != sig)
errAbort("%s is not a %s file", fileName, typeName);
}
bbi->typeSig = sig;
bbi->isSwapped = isSwapped;
/* Read rest of defined bits of header, byte swapping as needed. */
bbi->version = udcReadBits16(udc, isSwapped);
bbi->zoomLevels = udcReadBits16(udc, isSwapped);
bbi->chromTreeOffset = udcReadBits64(udc, isSwapped);
bbi->unzoomedDataOffset = udcReadBits64(udc, isSwapped);
bbi->unzoomedIndexOffset = udcReadBits64(udc, isSwapped);
bbi->fieldCount = udcReadBits16(udc, isSwapped);
bbi->definedFieldCount = udcReadBits16(udc, isSwapped);
bbi->asOffset = udcReadBits64(udc, isSwapped);
bbi->totalSummaryOffset = udcReadBits64(udc, isSwapped);
bbi->uncompressBufSize = udcReadBits32(udc, isSwapped);
bbi->extensionOffset = udcReadBits64(udc, isSwapped);
/* Read zoom headers. */
int i;
struct bbiZoomLevel *level, *levelList = NULL;
for (i=0; i<bbi->zoomLevels; ++i)
{
AllocVar(level);
level->reductionLevel = udcReadBits32(udc, isSwapped);
level->reserved = udcReadBits32(udc, isSwapped);
level->dataOffset = udcReadBits64(udc, isSwapped);
level->indexOffset = udcReadBits64(udc, isSwapped);
slAddHead(&levelList, level);
}
slReverse(&levelList);
bbi->levelList = levelList;
/* Deal with header extension if any. */
if (bbi->extensionOffset != 0)
{
udcSeek(udc, bbi->extensionOffset);
bbi->extensionSize = udcReadBits16(udc, isSwapped);
bbi->extraIndexCount = udcReadBits16(udc, isSwapped);
bbi->extraIndexListOffset = udcReadBits64(udc, isSwapped);
}
/* Attach B+ tree of chromosome names and ids. */
udcSeek(udc, bbi->chromTreeOffset);
bbi->chromBpt = bptFileAttach(fileName, udc);
return bbi;
}
static void rFindOverlappingBlocks(struct cirTreeFile *crt, int level, bits64 indexFileOffset,
bits32 chromIx, bits32 start, bits32 end, struct fileOffsetSize **retList)
/* Recursively find blocks with data. */
{
struct udcFile *udc = crt->udc;
/* Seek to start of block. */
udcSeek(udc, indexFileOffset);
/* Read block header. */
UBYTE isLeaf;
UBYTE reserved;
bits16 i, childCount;
udcMustReadOne(udc, isLeaf);
udcMustReadOne(udc, reserved);
boolean isSwapped = crt->isSwapped;
childCount = udcReadBits16(udc, isSwapped);
verbose(3, "rFindOverlappingBlocks %llu %u:%u-%u. childCount %d. isLeaf %d\n", indexFileOffset, chromIx, start, end, (int)childCount, (int)isLeaf);
if (isLeaf)
{
/* Loop through node adding overlapping leaves to block list. */
for (i=0; i<childCount; ++i)
{
bits32 startChromIx = udcReadBits32(udc, isSwapped);
bits32 startBase = udcReadBits32(udc, isSwapped);
bits32 endChromIx = udcReadBits32(udc, isSwapped);
bits32 endBase = udcReadBits32(udc, isSwapped);
bits64 offset = udcReadBits64(udc, isSwapped);
bits64 size = udcReadBits64(udc, isSwapped);
if (cirTreeOverlaps(chromIx, start, end, startChromIx, startBase, endChromIx, endBase))
{
struct fileOffsetSize *block;
AllocVar(block);
block->offset = offset;
block->size = size;
slAddHead(retList, block);
}
}
}
else
{
/* Read node into arrays. */
bits32 startChromIx[childCount], startBase[childCount];
bits32 endChromIx[childCount], endBase[childCount];
bits64 offset[childCount];
for (i=0; i<childCount; ++i)
{
startChromIx[i] = udcReadBits32(udc, isSwapped);
startBase[i] = udcReadBits32(udc, isSwapped);
endChromIx[i] = udcReadBits32(udc, isSwapped);
endBase[i] = udcReadBits32(udc, isSwapped);
offset[i] = udcReadBits64(udc, isSwapped);
}
/* Recurse into child nodes that we overlap. */
for (i=0; i<childCount; ++i)
{
if (cirTreeOverlaps(chromIx, start, end, startChromIx[i], startBase[i],
endChromIx[i], endBase[i]))
{
rFindOverlappingBlocks(crt, level+1, offset[i], chromIx, start, end, retList);
}
}
}
}
bits64 bigBedItemCount(struct bbiFile *bbi)
/* Return total items in file. */
{
udcSeek(bbi->udc, bbi->unzoomedDataOffset);
return udcReadBits64(bbi->udc, bbi->isSwapped);
}
struct bbiSummaryElement bbiTotalSummary(struct bbiFile *bbi)
/* Return summary of entire file! */
{
struct udcFile *udc = bbi->udc;
boolean isSwapped = bbi->isSwapped;
struct bbiSummaryElement res;
ZeroVar(&res);
if (bbi->totalSummaryOffset != 0)
{
udcSeek(udc, bbi->totalSummaryOffset);
res.validCount = udcReadBits64(udc, isSwapped);
res.minVal = udcReadDouble(udc, isSwapped);
res.maxVal = udcReadDouble(udc, isSwapped);
res.sumData = udcReadDouble(udc, isSwapped);
res.sumSquares = udcReadDouble(udc, isSwapped);
}
else if (bbi->version == 1)
/* Require version 1 so as not to have to deal with compression. Should not happen
* to have NULL totalSummaryOffset for non-empty version 2+ file anyway. */
{
/* Find most extreme zoom. */
struct bbiZoomLevel *bestZoom = NULL, *zoom;
bits32 bestReduction = 0;
for (zoom = bbi->levelList; zoom != NULL; zoom = zoom->next)
{
if (zoom->reductionLevel > bestReduction)
{
bestReduction = zoom->reductionLevel;
bestZoom = zoom;
}
}
if (bestZoom != NULL)
{
udcSeek(udc, bestZoom->dataOffset);
bits32 zoomSectionCount = udcReadBits32(udc, isSwapped);
bits32 i;
for (i=0; i<zoomSectionCount; ++i)
{
/* Read, but ignore, position. */
bits32 chromId, chromStart, chromEnd;
chromId = udcReadBits32(udc, isSwapped);
chromStart = udcReadBits32(udc, isSwapped);
chromEnd = udcReadBits32(udc, isSwapped);
/* First time through set values, rest of time add to them. */
if (i == 0)
{
res.validCount = udcReadBits32(udc, isSwapped);
res.minVal = udcReadFloat(udc, isSwapped);
res.maxVal = udcReadFloat(udc, isSwapped);
res.sumData = udcReadFloat(udc, isSwapped);
res.sumSquares = udcReadFloat(udc, isSwapped);
}
else
{
res.validCount += udcReadBits32(udc, isSwapped);
float minVal = udcReadFloat(udc, isSwapped);
if (minVal < res.minVal) res.minVal = minVal;
float maxVal = udcReadFloat(udc, isSwapped);
if (maxVal > res.maxVal) res.maxVal = maxVal;
res.sumData += udcReadFloat(udc, isSwapped);
res.sumSquares += udcReadFloat(udc, isSwapped);
}
}
}
}
return res;
}
struct bbiFile *bbiFileOpen(char *fileName, bits32 sig, char *typeName)
/* Open up big wig or big bed file. */
{
/* This code needs to agree with code in two other places currently - bigBedFileCreate,
* and bigWigFileCreate. I'm thinking of refactoring to share at least between
* bigBedFileCreate and bigWigFileCreate. It'd be great so it could be structured
* so that it could send the input in one chromosome at a time, and send in the zoom
* stuff only after all the chromosomes are done. This'd potentially reduce the memory
* footprint by a factor of 2 or 4. Still, for now it works. -JK */
struct bbiFile *bbi;
AllocVar(bbi);
bbi->fileName = cloneString(fileName);
struct udcFile *udc = bbi->udc = udcFileOpen(fileName, udcDefaultDir());
/* 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;
udcMustRead(udc, &magic, sizeof(magic));
if (magic != sig)
{
magic = byteSwap32(magic);
isSwapped = TRUE;
if (magic != sig)
errAbort("%s is not a %s file", fileName, typeName);
}
bbi->typeSig = sig;
bbi->isSwapped = isSwapped;
/* Read rest of defined bits of header, byte swapping as needed. */
bbi->version = udcReadBits16(udc, isSwapped);
bbi->zoomLevels = udcReadBits16(udc, isSwapped);
bbi->chromTreeOffset = udcReadBits64(udc, isSwapped);
bbi->unzoomedDataOffset = udcReadBits64(udc, isSwapped);
bbi->unzoomedIndexOffset = udcReadBits64(udc, isSwapped);
bbi->fieldCount = udcReadBits16(udc, isSwapped);
bbi->definedFieldCount = udcReadBits16(udc, isSwapped);
bbi->asOffset = udcReadBits64(udc, isSwapped);
bbi->totalSummaryOffset = udcReadBits64(udc, isSwapped);
bbi->uncompressBufSize = udcReadBits32(udc, isSwapped);
/* Skip over reserved area. */
udcSeek(udc, 64);
/* Read zoom headers. */
int i;
struct bbiZoomLevel *level, *levelList = NULL;
for (i=0; i<bbi->zoomLevels; ++i)
{
AllocVar(level);
level->reductionLevel = udcReadBits32(udc, isSwapped);
level->reserved = udcReadBits32(udc, isSwapped);
level->dataOffset = udcReadBits64(udc, isSwapped);
level->indexOffset = udcReadBits64(udc, isSwapped);
slAddHead(&levelList, level);
}
slReverse(&levelList);
bbi->levelList = levelList;
/* Attach B+ tree of chromosome names and ids. */
udcSeek(udc, bbi->chromTreeOffset);
bbi->chromBpt = bptFileAttach(fileName, udc);
return bbi;
}
