void bwgCreate(struct bwgSection *sectionList, struct hash *chromSizeHash,
int blockSize, int itemsPerSlot, boolean doCompress, boolean keepAllChromosomes,
boolean fixedSummaries, char *fileName)
/* Create a bigWig file out of a sorted sectionList. */
{
bits64 sectionCount = slCount(sectionList);
FILE *f = mustOpen(fileName, "wb");
bits32 sig = bigWigSig;
bits16 version = bbiCurrentVersion;
bits16 summaryCount = 0;
bits16 reserved16 = 0;
bits32 reserved32 = 0;
bits64 reserved64 = 0;
bits64 dataOffset = 0, dataOffsetPos;
bits64 indexOffset = 0, indexOffsetPos;
bits64 chromTreeOffset = 0, chromTreeOffsetPos;
bits64 totalSummaryOffset = 0, totalSummaryOffsetPos;
bits32 uncompressBufSize = 0;
bits64 uncompressBufSizePos;
struct bbiSummary *reduceSummaries[10];
bits32 reductionAmounts[10];
bits64 reductionDataOffsetPos[10];
bits64 reductionDataOffsets[10];
bits64 reductionIndexOffsets[10];
int i;
/* Figure out chromosome ID's. */
struct bbiChromInfo *chromInfoArray;
int chromCount, maxChromNameSize;
if (keepAllChromosomes)
bwgMakeAllChromInfo(sectionList, chromSizeHash, &chromCount, &chromInfoArray, &maxChromNameSize);
else
bwgMakeChromInfo(sectionList, chromSizeHash, &chromCount, &chromInfoArray, &maxChromNameSize);
if (fixedSummaries)
bwgComputeFixedSummaries(sectionList, reduceSummaries, &summaryCount, chromInfoArray, reductionAmounts);
else
bwgComputeDynamicSummaries(sectionList, reduceSummaries, &summaryCount, chromInfoArray, chromCount, reductionAmounts, doCompress);
/* Write fixed header. */
writeOne(f, sig);
writeOne(f, version);
writeOne(f, summaryCount);
chromTreeOffsetPos = ftell(f);
writeOne(f, chromTreeOffset);
dataOffsetPos = ftell(f);
writeOne(f, dataOffset);
indexOffsetPos = ftell(f);
writeOne(f, indexOffset);
writeOne(f, reserved16); /* fieldCount */
writeOne(f, reserved16); /* definedFieldCount */
writeOne(f, reserved64); /* autoSqlOffset. */
totalSummaryOffsetPos = ftell(f);
writeOne(f, totalSummaryOffset);
uncompressBufSizePos = ftell(f);
writeOne(f, uncompressBufSize);
writeOne(f, reserved64); /* nameIndexOffset */
assert(ftell(f) == 64);
/* Write summary headers */
for (i=0; i<summaryCount; ++i)
{
writeOne(f, reductionAmounts[i]);
writeOne(f, reserved32);
reductionDataOffsetPos[i] = ftell(f);
writeOne(f, reserved64); // Fill in with data offset later
writeOne(f, reserved64); // Fill in with index offset later
}
/* Write dummy summary */
struct bbiSummaryElement totalSum;
ZeroVar(&totalSum);
totalSummaryOffset = ftell(f);
bbiSummaryElementWrite(f, &totalSum);
/* Write chromosome bPlusTree */
chromTreeOffset = ftell(f);
int chromBlockSize = min(blockSize, chromCount);
bptFileBulkIndexToOpenFile(chromInfoArray, sizeof(chromInfoArray[0]), chromCount, chromBlockSize,
bbiChromInfoKey, maxChromNameSize, bbiChromInfoVal,
sizeof(chromInfoArray[0].id) + sizeof(chromInfoArray[0].size),
f);
/* Write out data section count and sections themselves. */
dataOffset = ftell(f);
writeOne(f, sectionCount);
struct bwgSection *section;
for (section = sectionList; section != NULL; section = section->next)
{
bits32 uncSizeOne = bwgSectionWrite(section, doCompress, f);
if (uncSizeOne > uncompressBufSize)
uncompressBufSize = uncSizeOne;
}
/* Write out index - creating a temporary array rather than list representation of
* sections in the process. */
indexOffset = ftell(f);
struct bwgSection **sectionArray;
AllocArray(sectionArray, sectionCount);
for (section = sectionList, i=0; section != NULL; section = section->next, ++i)
sectionArray[i] = section;
cirTreeFileBulkIndexToOpenFile(sectionArray, sizeof(sectionArray[0]), sectionCount,
blockSize, 1, NULL, bwgSectionFetchKey, bwgSectionFetchOffset,
indexOffset, f);
freez(§ionArray);
/* Write out summary sections. */
verbose(2, "bwgCreate writing %d summaries\n", summaryCount);
for (i=0; i<summaryCount; ++i)
{
reductionDataOffsets[i] = ftell(f);
reductionIndexOffsets[i] = bbiWriteSummaryAndIndex(reduceSummaries[i], blockSize, itemsPerSlot, doCompress, f);
verbose(3, "wrote %d of data, %d of index on level %d\n", (int)(reductionIndexOffsets[i] - reductionDataOffsets[i]), (int)(ftell(f) - reductionIndexOffsets[i]), i);
}
/* Calculate summary */
struct bbiSummary *sum = reduceSummaries[0];
if (sum != NULL)
{
totalSum.validCount = sum->validCount;
totalSum.minVal = sum->minVal;
totalSum.maxVal = sum->maxVal;
totalSum.sumData = sum->sumData;
totalSum.sumSquares = sum->sumSquares;
for (sum = sum->next; sum != NULL; sum = sum->next)
{
totalSum.validCount += sum->validCount;
if (sum->minVal < totalSum.minVal) totalSum.minVal = sum->minVal;
if (sum->maxVal > totalSum.maxVal) totalSum.maxVal = sum->maxVal;
totalSum.sumData += sum->sumData;
totalSum.sumSquares += sum->sumSquares;
}
/* Write real summary */
fseek(f, totalSummaryOffset, SEEK_SET);
bbiSummaryElementWrite(f, &totalSum);
}
else
totalSummaryOffset = 0; /* Edge case, no summary. */
/* Go back and fill in offsets properly in header. */
fseek(f, dataOffsetPos, SEEK_SET);
writeOne(f, dataOffset);
fseek(f, indexOffsetPos, SEEK_SET);
writeOne(f, indexOffset);
fseek(f, chromTreeOffsetPos, SEEK_SET);
writeOne(f, chromTreeOffset);
fseek(f, totalSummaryOffsetPos, SEEK_SET);
writeOne(f, totalSummaryOffset);
if (doCompress)
{
int maxZoomUncompSize = itemsPerSlot * sizeof(struct bbiSummaryOnDisk);
if (maxZoomUncompSize > uncompressBufSize)
uncompressBufSize = maxZoomUncompSize;
fseek(f, uncompressBufSizePos, SEEK_SET);
writeOne(f, uncompressBufSize);
}
/* Also fill in offsets in zoom headers. */
for (i=0; i<summaryCount; ++i)
{
fseek(f, reductionDataOffsetPos[i], SEEK_SET);
writeOne(f, reductionDataOffsets[i]);
writeOne(f, reductionIndexOffsets[i]);
}
/* Write end signature. */
fseek(f, 0L, SEEK_END);
writeOne(f, sig);
/* Clean up */
freez(&chromInfoArray);
carefulClose(&f);
}
void bwgCreate(struct bwgSection *sectionList, struct hash *chromSizeHash,
int blockSize, int itemsPerSlot, boolean doCompress, char *fileName)
/* Create a bigWig file out of a sorted sectionList. */
{
bits64 sectionCount = slCount(sectionList);
FILE *f = mustOpen(fileName, "wb");
bits32 sig = bigWigSig;
bits16 version = bbiCurrentVersion;
bits16 summaryCount = 0;
bits16 reserved16 = 0;
bits32 reserved32 = 0;
bits64 reserved64 = 0;
bits64 dataOffset = 0, dataOffsetPos;
bits64 indexOffset = 0, indexOffsetPos;
bits64 chromTreeOffset = 0, chromTreeOffsetPos;
bits64 totalSummaryOffset = 0, totalSummaryOffsetPos;
bits32 uncompressBufSize = 0;
bits64 uncompressBufSizePos;
struct bbiSummary *reduceSummaries[10];
bits32 reductionAmounts[10];
bits64 reductionDataOffsetPos[10];
bits64 reductionDataOffsets[10];
bits64 reductionIndexOffsets[10];
int i;
/* Figure out chromosome ID's. */
struct bbiChromInfo *chromInfoArray;
int chromCount, maxChromNameSize;
bwgMakeChromInfo(sectionList, chromSizeHash, &chromCount, &chromInfoArray, &maxChromNameSize);
/* Figure out initial summary level - starting with a summary 10 times the amount
* of the smallest item. See if summarized data is smaller than half input data, if
* not bump up reduction by a factor of 2 until it is, or until further summarying
* yeilds no size reduction. */
int minRes = bwgAverageResolution(sectionList);
int initialReduction = minRes*10;
bits64 fullSize = bwgTotalSectionSize(sectionList);
bits64 maxReducedSize = fullSize/2;
struct bbiSummary *firstSummaryList = NULL, *summaryList = NULL;
bits64 lastSummarySize = 0, summarySize;
for (;;)
{
summaryList = bwgReduceSectionList(sectionList, chromInfoArray, initialReduction);
bits64 summarySize = bbiTotalSummarySize(summaryList);
if (doCompress)
{
summarySize *= 2; // Compensate for summary not compressing as well as primary data
}
if (summarySize >= maxReducedSize && summarySize != lastSummarySize)
{
/* Need to do more reduction. First scale reduction by amount that it missed
* being small enough last time, with an extra 10% for good measure. Then
* just to keep from spinning through loop two many times, make sure this is
* at least 2x the previous reduction. */
int nextReduction = 1.1 * initialReduction * summarySize / maxReducedSize;
if (nextReduction < initialReduction*2)
nextReduction = initialReduction*2;
initialReduction = nextReduction;
bbiSummaryFreeList(&summaryList);
lastSummarySize = summarySize;
}
else
break;
}
summaryCount = 1;
reduceSummaries[0] = firstSummaryList = summaryList;
reductionAmounts[0] = initialReduction;
/* Now calculate up to 10 levels of further summary. */
bits64 reduction = initialReduction;
for (i=0; i<ArraySize(reduceSummaries)-1; i++)
{
reduction *= 4;
if (reduction > 1000000000)
break;
summaryList = bbiReduceSummaryList(reduceSummaries[summaryCount-1], chromInfoArray,
reduction);
summarySize = bbiTotalSummarySize(summaryList);
if (summarySize != lastSummarySize)
{
reduceSummaries[summaryCount] = summaryList;
reductionAmounts[summaryCount] = reduction;
++summaryCount;
}
int summaryItemCount = slCount(summaryList);
if (summaryItemCount <= chromCount)
break;
}
/* Write fixed header. */
writeOne(f, sig);
writeOne(f, version);
writeOne(f, summaryCount);
chromTreeOffsetPos = ftell(f);
writeOne(f, chromTreeOffset);
dataOffsetPos = ftell(f);
writeOne(f, dataOffset);
indexOffsetPos = ftell(f);
writeOne(f, indexOffset);
writeOne(f, reserved16); /* fieldCount */
writeOne(f, reserved16); /* definedFieldCount */
writeOne(f, reserved64); /* autoSqlOffset. */
totalSummaryOffsetPos = ftell(f);
writeOne(f, totalSummaryOffset);
uncompressBufSizePos = ftell(f);
writeOne(f, uncompressBufSize);
writeOne(f, reserved64); /* nameIndexOffset */
assert(ftell(f) == 64);
/* Write summary headers */
for (i=0; i<summaryCount; ++i)
{
writeOne(f, reductionAmounts[i]);
writeOne(f, reserved32);
reductionDataOffsetPos[i] = ftell(f);
writeOne(f, reserved64); // Fill in with data offset later
writeOne(f, reserved64); // Fill in with index offset later
}
/* Write dummy summary */
struct bbiSummaryElement totalSum;
ZeroVar(&totalSum);
totalSummaryOffset = ftell(f);
bbiSummaryElementWrite(f, &totalSum);
/* Write chromosome bPlusTree */
chromTreeOffset = ftell(f);
int chromBlockSize = min(blockSize, chromCount);
bptFileBulkIndexToOpenFile(chromInfoArray, sizeof(chromInfoArray[0]), chromCount, chromBlockSize,
bbiChromInfoKey, maxChromNameSize, bbiChromInfoVal,
sizeof(chromInfoArray[0].id) + sizeof(chromInfoArray[0].size),
f);
/* Write out data section count and sections themselves. */
dataOffset = ftell(f);
writeOne(f, sectionCount);
struct bwgSection *section;
for (section = sectionList; section != NULL; section = section->next)
{
bits32 uncSizeOne = bwgSectionWrite(section, doCompress, f);
if (uncSizeOne > uncompressBufSize)
uncompressBufSize = uncSizeOne;
}
/* Write out index - creating a temporary array rather than list representation of
* sections in the process. */
indexOffset = ftell(f);
struct bwgSection **sectionArray;
AllocArray(sectionArray, sectionCount);
for (section = sectionList, i=0; section != NULL; section = section->next, ++i)
sectionArray[i] = section;
cirTreeFileBulkIndexToOpenFile(sectionArray, sizeof(sectionArray[0]), sectionCount,
blockSize, 1, NULL, bwgSectionFetchKey, bwgSectionFetchOffset,
indexOffset, f);
freez(§ionArray);
/* Write out summary sections. */
verbose(2, "bwgCreate writing %d summaries\n", summaryCount);
for (i=0; i<summaryCount; ++i)
{
reductionDataOffsets[i] = ftell(f);
reductionIndexOffsets[i] = bbiWriteSummaryAndIndex(reduceSummaries[i], blockSize, itemsPerSlot, doCompress, f);
verbose(3, "wrote %d of data, %d of index on level %d\n", (int)(reductionIndexOffsets[i] - reductionDataOffsets[i]), (int)(ftell(f) - reductionIndexOffsets[i]), i);
}
/* Calculate summary */
struct bbiSummary *sum = firstSummaryList;
if (sum != NULL)
{
totalSum.validCount = sum->validCount;
totalSum.minVal = sum->minVal;
totalSum.maxVal = sum->maxVal;
totalSum.sumData = sum->sumData;
totalSum.sumSquares = sum->sumSquares;
for (sum = sum->next; sum != NULL; sum = sum->next)
{
totalSum.validCount += sum->validCount;
if (sum->minVal < totalSum.minVal) totalSum.minVal = sum->minVal;
if (sum->maxVal > totalSum.maxVal) totalSum.maxVal = sum->maxVal;
totalSum.sumData += sum->sumData;
totalSum.sumSquares += sum->sumSquares;
}
/* Write real summary */
fseek(f, totalSummaryOffset, SEEK_SET);
bbiSummaryElementWrite(f, &totalSum);
}
else
totalSummaryOffset = 0; /* Edge case, no summary. */
/* Go back and fill in offsets properly in header. */
fseek(f, dataOffsetPos, SEEK_SET);
writeOne(f, dataOffset);
fseek(f, indexOffsetPos, SEEK_SET);
writeOne(f, indexOffset);
fseek(f, chromTreeOffsetPos, SEEK_SET);
writeOne(f, chromTreeOffset);
fseek(f, totalSummaryOffsetPos, SEEK_SET);
writeOne(f, totalSummaryOffset);
if (doCompress)
{
int maxZoomUncompSize = itemsPerSlot * sizeof(struct bbiSummaryOnDisk);
if (maxZoomUncompSize > uncompressBufSize)
uncompressBufSize = maxZoomUncompSize;
fseek(f, uncompressBufSizePos, SEEK_SET);
writeOne(f, uncompressBufSize);
}
/* Also fill in offsets in zoom headers. */
for (i=0; i<summaryCount; ++i)
{
fseek(f, reductionDataOffsetPos[i], SEEK_SET);
writeOne(f, reductionDataOffsets[i]);
writeOne(f, reductionIndexOffsets[i]);
}
/* Write end signature. */
fseek(f, 0L, SEEK_END);
writeOne(f, sig);
/* Clean up */
freez(&chromInfoArray);
carefulClose(&f);
}
void bbFileCreate(
char *inName, /* Input file in a tabular bed format <chrom><start><end> + whatever. */
char *chromSizes, /* Two column tab-separated file: <chromosome> <size>. */
int blockSize, /* Number of items to bundle in r-tree. 1024 is good. */
int itemsPerSlot, /* Number of items in lowest level of tree. 64 is good. */
char *asText, /* Field definitions in a string */
struct asObject *as, /* Field definitions parsed out */
boolean doCompress, /* If TRUE then compress data. */
struct slName *extraIndexList, /* List of extra indexes to add */
char *outName) /* BigBed output file name. */
/* Convert tab-separated bed file to binary indexed, zoomed bigBed version. */
{
/* Set up timing measures. */
verboseTimeInit();
struct lineFile *lf = lineFileOpen(inName, TRUE);
bits16 fieldCount = slCount(as->columnList);
bits16 extraIndexCount = slCount(extraIndexList);
struct bbExIndexMaker *eim = NULL;
if (extraIndexList != NULL)
eim = bbExIndexMakerNew(extraIndexList, as);
/* Load in chromosome sizes. */
struct hash *chromSizesHash = NULL;
if (sizesIs2Bit)
chromSizesHash = twoBitChromHash(chromSizes);
else
chromSizesHash = bbiChromSizesFromFile(chromSizes);
verbose(2, "Read %d chromosomes and sizes from %s\n", chromSizesHash->elCount, chromSizes);
/* Do first pass, mostly just scanning file and counting hits per chromosome. */
int minDiff = 0;
double aveSize = 0;
bits64 bedCount = 0;
bits32 uncompressBufSize = 0;
struct bbiChromUsage *usageList = bbiChromUsageFromBedFile(lf, chromSizesHash, eim,
&minDiff, &aveSize, &bedCount, tabSep);
verboseTime(1, "pass1 - making usageList (%d chroms)", slCount(usageList));
verbose(2, "%d chroms in %s. Average span of beds %f\n", slCount(usageList), inName, aveSize);
/* Open output file and write dummy header. */
FILE *f = mustOpen(outName, "wb");
bbiWriteDummyHeader(f);
bbiWriteDummyZooms(f);
/* Write out autoSql string */
bits64 asOffset = ftell(f);
mustWrite(f, asText, strlen(asText) + 1);
verbose(2, "as definition has %d columns\n", fieldCount);
/* Write out dummy total summary. */
struct bbiSummaryElement totalSum;
ZeroVar(&totalSum);
bits64 totalSummaryOffset = ftell(f);
bbiSummaryElementWrite(f, &totalSum);
/* Write out dummy header extension */
bits64 extHeaderOffset = ftell(f);
bits16 extHeaderSize = 64;
repeatCharOut(f, 0, extHeaderSize);
/* Write out extra index stuff if need be. */
bits64 extraIndexListOffset = 0;
bits64 extraIndexListEndOffset = 0;
if (extraIndexList != NULL)
{
extraIndexListOffset = ftell(f);
int extraIndexSize = 16 + 4*1; // Fixed record size 16, plus 1 times field size of 4
repeatCharOut(f, 0, extraIndexSize*extraIndexCount);
extraIndexListEndOffset = ftell(f);
}
/* Write out chromosome/size database. */
bits64 chromTreeOffset = ftell(f);
bbiWriteChromInfo(usageList, blockSize, f);
/* Set up to keep track of possible initial reduction levels. */
int resScales[bbiMaxZoomLevels], resSizes[bbiMaxZoomLevels];
int resTryCount = bbiCalcResScalesAndSizes(aveSize, resScales, resSizes);
/* Write out primary full resolution data in sections, collect stats to use for reductions. */
bits64 dataOffset = ftell(f);
bits32 blockCount = 0;
bits32 maxBlockSize = 0;
struct bbiBoundsArray *boundsArray = NULL;
writeOne(f, bedCount);
if (bedCount > 0)
{
blockCount = bbiCountSectionsNeeded(usageList, itemsPerSlot);
AllocArray(boundsArray, blockCount);
lineFileRewind(lf);
if (eim)
bbExIndexMakerAllocChunkArrays(eim, bedCount);
writeBlocks(usageList, lf, as, itemsPerSlot, boundsArray, blockCount, doCompress,
f, resTryCount, resScales, resSizes, eim, bedCount, fieldCount, &maxBlockSize);
}
verboseTime(1, "pass2 - checking and writing primary data (%lld records, %d fields)",
(long long)bedCount, fieldCount);
/* Write out primary data index. */
bits64 indexOffset = ftell(f);
cirTreeFileBulkIndexToOpenFile(boundsArray, sizeof(boundsArray[0]), blockCount,
blockSize, 1, NULL, bbiBoundsArrayFetchKey, bbiBoundsArrayFetchOffset,
indexOffset, f);
freez(&boundsArray);
verboseTime(2, "index write");
/* Declare arrays and vars that track the zoom levels we actually output. */
bits32 zoomAmounts[bbiMaxZoomLevels];
bits64 zoomDataOffsets[bbiMaxZoomLevels];
bits64 zoomIndexOffsets[bbiMaxZoomLevels];
/* Call monster zoom maker library function that bedGraphToBigWig also uses. */
int zoomLevels = 0;
if (bedCount > 0)
{
zoomLevels = bbiWriteZoomLevels(lf, f, blockSize, itemsPerSlot,
bedWriteReducedOnceReturnReducedTwice, fieldCount,
doCompress, indexOffset - dataOffset,
usageList, resTryCount, resScales, resSizes,
zoomAmounts, zoomDataOffsets, zoomIndexOffsets, &totalSum);
}
/* Write out extra indexes if need be. */
if (eim)
{
int i;
for (i=0; i < eim->indexCount; ++i)
{
eim->fileOffsets[i] = ftell(f);
maxBedNameSize = eim->maxFieldSize[i];
qsort(eim->chunkArrayArray[i], bedCount,
sizeof(struct bbNamedFileChunk), bbNamedFileChunkCmpByName);
assert(sizeof(struct bbNamedFileChunk) == sizeof(eim->chunkArrayArray[i][0]));
bptFileBulkIndexToOpenFile(eim->chunkArrayArray[i], sizeof(eim->chunkArrayArray[i][0]),
bedCount, blockSize, bbNamedFileChunkKey, maxBedNameSize, bbNamedFileChunkVal,
sizeof(bits64) + sizeof(bits64), f);
verboseTime(1, "Sorting and writing extra index %d", i);
}
}
/* Figure out buffer size needed for uncompression if need be. */
if (doCompress)
{
int maxZoomUncompSize = itemsPerSlot * sizeof(struct bbiSummaryOnDisk);
uncompressBufSize = max(maxBlockSize, maxZoomUncompSize);
}
/* Go back and rewrite header. */
rewind(f);
bits32 sig = bigBedSig;
bits16 version = bbiCurrentVersion;
bits16 summaryCount = zoomLevels;
bits32 reserved32 = 0;
bits64 reserved64 = 0;
bits16 definedFieldCount = bedN;
/* Write fixed header */
writeOne(f, sig);
writeOne(f, version);
writeOne(f, summaryCount);
writeOne(f, chromTreeOffset);
writeOne(f, dataOffset);
writeOne(f, indexOffset);
writeOne(f, fieldCount);
writeOne(f, definedFieldCount);
writeOne(f, asOffset);
writeOne(f, totalSummaryOffset);
writeOne(f, uncompressBufSize);
writeOne(f, extHeaderOffset);
assert(ftell(f) == 64);
/* Write summary headers with data. */
int i;
verbose(2, "Writing %d levels of zoom\n", zoomLevels);
for (i=0; i<zoomLevels; ++i)
{
verbose(3, "zoomAmounts[%d] = %d\n", i, (int)zoomAmounts[i]);
writeOne(f, zoomAmounts[i]);
writeOne(f, reserved32);
writeOne(f, zoomDataOffsets[i]);
writeOne(f, zoomIndexOffsets[i]);
}
/* Write rest of summary headers with no data. */
for (i=zoomLevels; i<bbiMaxZoomLevels; ++i)
{
writeOne(f, reserved32);
writeOne(f, reserved32);
writeOne(f, reserved64);
writeOne(f, reserved64);
}
/* Write total summary. */
fseek(f, totalSummaryOffset, SEEK_SET);
bbiSummaryElementWrite(f, &totalSum);
/* Write extended header */
fseek(f, extHeaderOffset, SEEK_SET);
writeOne(f, extHeaderSize);
writeOne(f, extraIndexCount);
writeOne(f, extraIndexListOffset);
repeatCharOut(f, 0, 52); // reserved
assert(ftell(f) - extHeaderOffset == extHeaderSize);
/* Write extra index offsets if need be. */
if (extraIndexCount != 0)
{
fseek(f, extraIndexListOffset, SEEK_SET);
int i;
for (i=0; i<extraIndexCount; ++i)
{
// Write out fixed part of index info
bits16 type = 0; // bPlusTree type
bits16 indexFieldCount = 1;
writeOne(f, type);
writeOne(f, indexFieldCount);
writeOne(f, eim->fileOffsets[i]);
repeatCharOut(f, 0, 4); // reserved
// Write out field list - easy this time because for now always only one field.
bits16 fieldId = eim->indexFields[i];
writeOne(f, fieldId);
repeatCharOut(f, 0, 2); // reserved
}
assert(ftell(f) == extraIndexListEndOffset);
}
/* Write end signature. */
fseek(f, 0L, SEEK_END);
writeOne(f, sig);
/* Clean up. */
lineFileClose(&lf);
carefulClose(&f);
freeHash(&chromSizesHash);
bbiChromUsageFreeList(&usageList);
asObjectFreeList(&as);
}
void bedGraphToBigWig(char *inName, char *chromSizes, char *outName)
/* bedGraphToBigWig - Convert a bedGraph program to bigWig.. */
{
verboseTimeInit();
struct lineFile *lf = lineFileOpen(inName, TRUE);
struct hash *chromSizesHash = bbiChromSizesFromFile(chromSizes);
verbose(2, "%d chroms in %s\n", chromSizesHash->elCount, chromSizes);
int minDiff = 0, i;
double aveSize = 0;
bits64 bedCount = 0;
bits32 uncompressBufSize = 0;
struct bbiChromUsage *usageList = bbiChromUsageFromBedFile(lf, chromSizesHash, NULL,
&minDiff, &aveSize, &bedCount);
verboseTime(2, "pass1");
verbose(2, "%d chroms in %s, minDiff=%d, aveSize=%g, bedCount=%lld\n",
slCount(usageList), inName, minDiff, aveSize, bedCount);
/* Write out dummy header, zoom offsets. */
FILE *f = mustOpen(outName, "wb");
bbiWriteDummyHeader(f);
bbiWriteDummyZooms(f);
/* Write out dummy total summary. */
struct bbiSummaryElement totalSum;
ZeroVar(&totalSum);
bits64 totalSummaryOffset = ftell(f);
bbiSummaryElementWrite(f, &totalSum);
/* Write out chromosome/size database. */
bits64 chromTreeOffset = ftell(f);
bbiWriteChromInfo(usageList, blockSize, f);
/* Set up to keep track of possible initial reduction levels. */
int resScales[bbiMaxZoomLevels], resSizes[bbiMaxZoomLevels];
int resTryCount = bbiCalcResScalesAndSizes(aveSize, resScales, resSizes);
/* Write out primary full resolution data in sections, collect stats to use for reductions. */
bits64 dataOffset = ftell(f);
bits64 sectionCount = bbiCountSectionsNeeded(usageList, itemsPerSlot);
writeOne(f, sectionCount);
struct bbiBoundsArray *boundsArray;
AllocArray(boundsArray, sectionCount);
lineFileRewind(lf);
bits32 maxSectionSize = 0;
writeSections(usageList, lf, itemsPerSlot, boundsArray, sectionCount, f,
resTryCount, resScales, resSizes, doCompress, &maxSectionSize);
verboseTime(2, "pass2");
/* Write out primary data index. */
bits64 indexOffset = ftell(f);
cirTreeFileBulkIndexToOpenFile(boundsArray, sizeof(boundsArray[0]), sectionCount,
blockSize, 1, NULL, bbiBoundsArrayFetchKey, bbiBoundsArrayFetchOffset,
indexOffset, f);
verboseTime(2, "index write");
/* Declare arrays and vars that track the zoom levels we actually output. */
bits32 zoomAmounts[bbiMaxZoomLevels];
bits64 zoomDataOffsets[bbiMaxZoomLevels];
bits64 zoomIndexOffsets[bbiMaxZoomLevels];
/* Call monster zoom maker library function that bedToBigBed also uses. */
int zoomLevels = bbiWriteZoomLevels(lf, f, blockSize, itemsPerSlot,
bedGraphWriteReducedOnceReturnReducedTwice, 4,
doCompress, indexOffset - dataOffset,
usageList, resTryCount, resScales, resSizes,
zoomAmounts, zoomDataOffsets, zoomIndexOffsets, &totalSum);
/* Figure out buffer size needed for uncompression if need be. */
if (doCompress)
{
int maxZoomUncompSize = itemsPerSlot * sizeof(struct bbiSummaryOnDisk);
uncompressBufSize = max(maxSectionSize, maxZoomUncompSize);
}
/* Go back and rewrite header. */
rewind(f);
bits32 sig = bigWigSig;
bits16 version = bbiCurrentVersion;
bits16 summaryCount = zoomLevels;
bits16 reserved16 = 0;
bits32 reserved32 = 0;
bits64 reserved64 = 0;
/* Write fixed header */
writeOne(f, sig);
writeOne(f, version);
writeOne(f, summaryCount);
writeOne(f, chromTreeOffset);
writeOne(f, dataOffset);
writeOne(f, indexOffset);
writeOne(f, reserved16); // fieldCount
writeOne(f, reserved16); // definedFieldCount
writeOne(f, reserved64); // autoSqlOffset
writeOne(f, totalSummaryOffset);
writeOne(f, uncompressBufSize);
writeOne(f, reserved64); // nameIndexOffset
assert(ftell(f) == 64);
/* Write summary headers with data. */
verbose(2, "Writing %d levels of zoom\n", zoomLevels);
for (i=0; i<zoomLevels; ++i)
{
verbose(3, "zoomAmounts[%d] = %d\n", i, (int)zoomAmounts[i]);
writeOne(f, zoomAmounts[i]);
writeOne(f, reserved32);
writeOne(f, zoomDataOffsets[i]);
writeOne(f, zoomIndexOffsets[i]);
}
/* Write rest of summary headers with no data. */
for (i=zoomLevels; i<bbiMaxZoomLevels; ++i)
{
writeOne(f, reserved32);
writeOne(f, reserved32);
writeOne(f, reserved64);
writeOne(f, reserved64);
}
/* Write total summary. */
fseek(f, totalSummaryOffset, SEEK_SET);
bbiSummaryElementWrite(f, &totalSum);
/* Write end signature. */
fseek(f, 0L, SEEK_END);
writeOne(f, sig);
lineFileClose(&lf);
carefulClose(&f);
}
