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 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;
}
struct bptFile *bptFileOpen(char *fileName)
/* Open up index file - reading header and verifying things. */
{
return bptFileAttach(cloneString(fileName), udcFileOpen(fileName, udcDefaultDir()));
}
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;
}
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;
}
