private MutableTranscriptRegion[] ReadCdnaMaps()
{
var cols = GetColumns("cDNA");
int numCdnaMaps = int.Parse(cols[1]);
if (numCdnaMaps == 0)
{
return(null);
}
var cdnaMaps = new MutableTranscriptRegion[numCdnaMaps];
var colIndex = 2;
for (var i = 0; i < numCdnaMaps; i++)
{
int start = int.Parse(cols[colIndex++]);
int end = int.Parse(cols[colIndex++]);
int cdnaStart = int.Parse(cols[colIndex++]);
int cdnaEnd = int.Parse(cols[colIndex++]);
cdnaMaps[i] = new MutableTranscriptRegion(TranscriptRegionType.Exon, 0, start, end, cdnaStart, cdnaEnd);
}
return(cdnaMaps);
}
private static List <MutableTranscriptRegion> AddGaps(this List <MutableTranscriptRegion> sortedRegions)
{
for (var i = 1; i < sortedRegions.Count; i++)
{
var prevRegion = sortedRegions[i - 1];
var region = sortedRegions[i];
int gapLength = CalculateGapLength(prevRegion, region);
if (gapLength == 0)
{
continue;
}
var gapRegion = new MutableTranscriptRegion(TranscriptRegionType.Gap, 0, prevRegion.End + 1, region.Start - 1);
sortedRegions.Insert(i, gapRegion);
i++;
}
return(sortedRegions);
}