// Gets chunks for specified ref seq index, start and end co-ordinate this method considers linear index also.
private static IList <Chunk> GetChunks(BAMReferenceIndexes refIndex, int start, int end)
{
var chunks = new List <Chunk>();
var binnumbers = Reg2Bins((uint)start, (uint)end);
var bins = refIndex.Bins.Where(B => binnumbers.Contains(B.BinNumber)).ToList();
// consider linear indexing only for the bins less than 4681.
foreach (var bin in bins.Where(B => B.BinNumber < 4681))
{
chunks.InsertRange(chunks.Count, bin.Chunks);
}
var index = start / (16 * 1024); // Linear indexing window size is 16K
if (refIndex.LinearOffsets.Count > index)
{
var offset = refIndex.LinearOffsets[index];
chunks =
chunks.Where(
C =>
C.ChunkEnd.CompressedBlockOffset > offset.CompressedBlockOffset ||
(C.ChunkEnd.CompressedBlockOffset == offset.CompressedBlockOffset &&
C.ChunkEnd.UncompressedBlockOffset > offset.UncompressedBlockOffset)).ToList();
}
// add chunks for the bin numbers greater than 4681.
foreach (var bin in bins.Where(B => B.BinNumber >= 4681))
{
chunks.InsertRange(chunks.Count, bin.Chunks);
}
return(SortAndMergeChunks(chunks));
}
// Gets all chunks for the specified ref sequence index.
private static IList <Chunk> GetChunks(BAMReferenceIndexes refIndex)
{
var chunks = new List <Chunk>();
foreach (var bin in refIndex.Bins)
{
chunks.InsertRange(chunks.Count, bin.Chunks);
}
return(SortAndMergeChunks(chunks));
}