/// <summary>
/// Merges regions that share start and end in the same bin
/// </summary>
private static void MergeRegionList(ref List <BamIndexRegion> regions)
{
// merge regions with overlapping bins in the list
int prevIndex = 0;
for (int currentIndex = 1; currentIndex < regions.Count; ++currentIndex)
{
if ((regions[prevIndex].End >> 16) == (regions[currentIndex].Begin >> 16))
{
regions[prevIndex] = new BamIndexRegion(regions[prevIndex].Begin, regions[currentIndex].End);
}
else
{
regions[++prevIndex] = regions[currentIndex];
}
}
// remove the remaining regions
int numMergedRegions = prevIndex + 1;
int numRegionsToDelete = regions.Count - numMergedRegions;
if (numRegionsToDelete > 0)
{
regions.RemoveRange(numMergedRegions, numRegionsToDelete);
}
}
/// <summary>
/// Reads a BAM index from the supplied filename
/// </summary>
/// <returns>true if the index was successfully loaded</returns>
public bool ReadIndex(string filename)
{
// check if the file exists
if (!File.Exists(filename))
{
return(false);
}
using (
BinaryReader reader =
new BinaryReader(new FileStream(filename, FileMode.Open, FileAccess.Read, FileShare.Read)))
{
// check to see if we have a proper BAM index signature
byte[] buffer = reader.ReadBytes(4);
string magicNumberString = Encoding.ASCII.GetString(buffer, 0, 4);
if (magicNumberString != BamConstants.BaiMagicNumber)
{
throw new InvalidDataException(
string.Format("ERROR: Expected the BAM index magic number to be {0}, but found {1}.",
BamConstants.BaiMagicNumber, magicNumberString));
}
// read the number of reference sequences
uint numReferenceSequences = reader.ReadUInt32();
// iterate over each reference sequence
_index.Clear();
for (uint refSeqIndex = 0; refSeqIndex < numReferenceSequences; ++refSeqIndex)
{
// =======================
// read the binning index
// =======================
BamReferenceIndex refIndex = new BamReferenceIndex();
// read the number of bins
uint numBins = reader.ReadUInt32();
// iterate over each bin in the regions dictionary
for (uint binIndex = 0; binIndex < numBins; ++binIndex)
{
// read the bin and the number of index regions
uint bin = reader.ReadUInt32();
uint numIndexRegions = reader.ReadUInt32();
// read all of the index regions
List <BamIndexRegion> bamIndexRegions = new List <BamIndexRegion>();
for (uint regionIndex = 0; regionIndex < numIndexRegions; ++regionIndex)
{
ulong begin = reader.ReadUInt64();
ulong end = reader.ReadUInt64();
BamIndexRegion indexRegion = new BamIndexRegion(begin, end);
bamIndexRegions.Add(indexRegion);
}
// add the index regions to our dictionary
refIndex.RegionsDictionary[bin] = bamIndexRegions;
}
// =====================
// read the linear index
// =====================
// read the linear index size
uint numOffsets = reader.ReadUInt32();
for (uint offsetIndex = 0; offsetIndex < numOffsets; ++offsetIndex)
{
refIndex.OffsetList.Add(reader.ReadUInt64());
}
// add the reference index
_index.Add(refIndex);
}
// read the number of unaligned reads without coordinates
_numUnalignedWithoutCoordinates = reader.ReadUInt64();
}
return(true);
}
