private List <MitoMapSvItem> ExtractSvItemFromDeletionsSingle(List <string> info)
{
var junctions = info[0].OptimizedSplit(':').Select(int.Parse).ToList();
var start = junctions[0] + 1;
var end = junctions[1] - 1;
if (end < start)
{
throw new ArgumentOutOfRangeException($"Deletions with end position smaller than start position: start: {start}, end: {end}");
}
var calculatedSize = end - start + 1;
var size = int.Parse(info[1].Substring(1));
if (size <= MitomapParsingParameters.LargeDeletionCutoff)
{
return(new List <MitoMapSvItem>());
}
if (calculatedSize != size)
{
Console.WriteLine($"Incorrect size of deleted region: size of {start}-{end} should be {calculatedSize}, provided size is {size}. Provided size is used.");
}
var refSequence = _sequenceProvider.Sequence.Substring(start - 1, size);
var newStart = _variantAligner.LeftAlign(start, refSequence, "").Item1;
if (start != newStart)
{
Console.WriteLine($"Deletion of {size} bps. Original start start position: {start}; new position after left-alignment {newStart}.");
}
var mitoMapSvItem = new MitoMapSvItem(_chromosome, newStart, newStart + size - 1, VariantType.deletion);
return(new List <MitoMapSvItem> {
mitoMapSvItem
});
}
// extract large insertions from this file
private List <MitoMapSvItem> ExtractSvItemFromSimpleInsertions(IReadOnlyList <string> info)
{
var mitoMapSvItems = new List <MitoMapSvItem>();
var altAlleleInfo = info[2];
var dLoopPattern = new Regex(@"(?<start>^\d+)-(?<end>(\d+)) D-Loop region");
var dLoopMatch = dLoopPattern.Match(altAlleleInfo);
// not a large insertion
if (!dLoopMatch.Success)
{
return(mitoMapSvItems);
}
var genomeStart = MitoDLoop.Start + int.Parse(dLoopMatch.Groups["start"].Value) - 1;
var genomeEnd = MitoDLoop.Start + int.Parse(dLoopMatch.Groups["end"].Value) - 1;
if (genomeEnd < genomeStart)
{
throw new ArgumentOutOfRangeException($"Duplication with end position smaller than start position: start: {genomeStart}, end: {genomeEnd}");
}
var size = genomeEnd - genomeStart + 1;
var refSequence = _sequenceProvider.Sequence.Substring(genomeStart - 1, size);
var leftAlignResults = _variantAligner.LeftAlign(genomeStart, refSequence, refSequence + refSequence); // duplication
var newStart = leftAlignResults.Item1;
if (genomeStart != newStart)
{
Console.WriteLine($"Duplication of {size} bps. Original start start position: {genomeStart}; new position after left-alignment {newStart}.");
}
var mitoMapSvItem = new MitoMapSvItem(_chromosome, newStart, newStart + size - 1, VariantType.duplication);
mitoMapSvItems.Add(mitoMapSvItem);
return(mitoMapSvItems);
}