public TranscriptRegion(TranscriptRegionType type, ushort id, int start, int end, int cdnaStart, int cdnaEnd)
{
Type = type;
Id = id;
Start = start;
End = end;
CdnaStart = cdnaStart;
CdnaEnd = cdnaEnd;
}
private static int FindLast(ITranscriptRegion[] regions, TranscriptRegionType desiredType, int startIndex,
int endIndex)
{
for (int i = endIndex; i >= startIndex; i--)
{
if (regions[i].Type == desiredType)
{
return(i);
}
}
return(-1);
}
public static ITranscriptRegion Read(BufferedBinaryReader reader)
{
TranscriptRegionType type = (TranscriptRegionType)reader.ReadByte();
ushort id = reader.ReadOptUInt16();
int genomicStart = reader.ReadOptInt32();
int genomicEnd = reader.ReadOptInt32();
int cdnaStart = reader.ReadOptInt32();
int cdnaEnd = reader.ReadOptInt32();
return(new TranscriptRegion(type, id, genomicStart, genomicEnd, cdnaStart, cdnaEnd));
}
private static (int Start, int End) FindDesiredRegionIds(this ITranscriptRegion[] regions,
TranscriptRegionType desiredType, int startIndex, int endIndex)
{
var regionStart = FindFirst(regions, desiredType, startIndex, endIndex);
var newStartIndex = regionStart != -1 ? regionStart : startIndex;
var regionEnd = FindLast(regions, desiredType, newStartIndex, endIndex);
var startId = regionStart == -1 ? -1 : regions[regionStart].Id;
var endId = regionEnd == -1 ? -1 : regions[regionEnd].Id;
if (endId < startId)
{
Swap.Int(ref startId, ref endId);
}
return(startId, endId);
}
private static List <MutableTranscriptRegion> AddCoords(this List <MutableTranscriptRegion> regions, TranscriptRegionType targetRegionType, bool onReverseStrand)
{
for (var regionIndex = 0; regionIndex < regions.Count; regionIndex++)
{
var region = regions[regionIndex];
if (region.Type != targetRegionType)
{
continue;
}
var coords = regions.GetExonCoords(regionIndex, onReverseStrand);
region.CdnaStart = coords.CdnaStart;
region.CdnaEnd = coords.CdnaEnd;
}
return(regions);
}
private static List <MutableTranscriptRegion> AddIds(this List <MutableTranscriptRegion> regions,
IReadOnlyList <IdInterval> intervals, TranscriptRegionType targetRegionType, TranscriptRegionType matchRegionType)
{
if (intervals == null)
{
return(regions);
}
foreach (var region in regions)
{
if (region.Type != targetRegionType)
{
continue;
}
int regionMidPoint = region.Start + (region.End - region.Start >> 1);
int index = intervals.BinarySearch(regionMidPoint);
if (index < 0)
{
continue;
}
var intron = intervals[index];
region.Type = matchRegionType;
region.Id = intron.Id;
}
return(regions);
}
