protected BAMIndexContent query(
final int referenceSequence, final int startPos, final int endPos) {
seek(4);
final List<Chunk> metaDataChunks = new ArrayList<Chunk>();
final int sequenceCount = readInteger();
if (referenceSequence >= sequenceCount) {
return null;
}
final BitSet regionBins = GenomicIndexUtil.regionToBins(startPos, endPos);
if (regionBins == null) {
return null;
}
skipToSequence(referenceSequence);
final int binCount = readInteger();
boolean metaDataSeen = false;
final Bin[] bins = new Bin[getMaxBinNumberForReference(referenceSequence) + 1];
for (int binNumber = 0; binNumber < binCount; binNumber++) {
final int indexBin = readInteger();
final int nChunks = readInteger();
List<Chunk> chunks = null;
// System.out.println("# bin[" + i + "] = " + indexBin + ", nChunks = " + nChunks);
Chunk lastChunk = null;
if (regionBins.get(indexBin)) {
chunks = new ArrayList<Chunk>(nChunks);
for (int ci = 0; ci < nChunks; ci++) {
final long chunkBegin = readLong();
final long chunkEnd = readLong();
lastChunk = new Chunk(chunkBegin, chunkEnd);
chunks.add(lastChunk);
}
} else if (indexBin == GenomicIndexUtil.MAX_BINS) {
// meta data - build the bin so that the count of bins is correct;
// but don't attach meta chunks to the bin, or normal queries will be off
for (int ci = 0; ci < nChunks; ci++) {
final long chunkBegin = readLong();
final long chunkEnd = readLong();
lastChunk = new Chunk(chunkBegin, chunkEnd);
metaDataChunks.add(lastChunk);
}
metaDataSeen = true;
continue; // don't create a Bin
} else {
skipBytes(16 * nChunks);
chunks = Collections.emptyList();
}
final Bin bin = new Bin(referenceSequence, indexBin);
bin.setChunkList(chunks);
bin.setLastChunk(lastChunk);
bins[indexBin] = bin;
}
final int nLinearBins = readInteger();
final int regionLinearBinStart = LinearIndex.convertToLinearIndexOffset(startPos);
final int regionLinearBinStop =
endPos > 0 ? LinearIndex.convertToLinearIndexOffset(endPos) : nLinearBins - 1;
final int actualStop = Math.min(regionLinearBinStop, nLinearBins - 1);
long[] linearIndexEntries = new long[0];
if (regionLinearBinStart < nLinearBins) {
linearIndexEntries = new long[actualStop - regionLinearBinStart + 1];
skipBytes(8 * regionLinearBinStart);
for (int linearBin = regionLinearBinStart; linearBin <= actualStop; linearBin++)
linearIndexEntries[linearBin - regionLinearBinStart] = readLong();
}
final LinearIndex linearIndex =
new LinearIndex(referenceSequence, regionLinearBinStart, linearIndexEntries);
return new BAMIndexContent(
referenceSequence,
bins,
binCount - (metaDataSeen ? 1 : 0),
new BAMIndexMetaData(metaDataChunks),
linearIndex);
}
