/// <summary>
/// Adds a link to the map if it passes the link filter criteria.
/// </summary>
/// <param name="tssMap">Tss map.</param>
/// <param name="LocusMap">Locus map.</param>
/// <param name="filter">Filter.</param>
/// <param name="link">Link.</param>
private static void AddLink(
ref TssRegulatoryMap tssMap,
ref LocusRegulatoryMap LocusMap,
MapLinkFilter filter,
MapLink link)
{
if (filter.IsValidLink(link.Strand, link.LinkLength, link.ConfidenceScore, link.Correlation))
{
filter.ApplyLinkFilterType(link, tssMap, LocusMap);
}
}
/// <summary>
/// Loads the map.
/// </summary>
/// <returns>The map.</returns>
/// <param name="mapFileName">Map file name.</param>
/// <param name="filter">Filter of map links.</param>
public static TssRegulatoryMap LoadMap(
string mapFileName,
MapLinkFilter filter)
{
using (TextReader tr = new StreamReader(mapFileName))
{
string line = null;
TssRegulatoryMap tssMap = new TssRegulatoryMap();
LocusRegulatoryMap LocusMap = new LocusRegulatoryMap();
while ((line = tr.ReadLine()) != null)
{
var fields = line.Split('\t');
var transcriptName = fields[3];
var confidence = double.Parse(fields[8]);
var correlation = double.Parse(fields[7]);
var distance = int.Parse(fields[9]);
var LocusName = fields[6];
var strand = fields[5];
var link = new MapLink
{
ConfidenceScore = confidence,
Correlation = correlation,
LinkLength = distance,
TranscriptName = transcriptName,
TssName = transcriptName,
LocusName = LocusName,
Strand = strand,
Chromosome = fields[0],
TssPosition = int.Parse(fields[1]),
HistoneName = fields[10],
GeneName = fields[11],
};
if ((filter.TranscriptSet == null || (filter.TranscriptSet != null && filter.TranscriptSet.Contains(transcriptName))) &&
(filter.LocusSet == null || (filter.LocusSet != null && filter.LocusSet.Contains(LocusName))))
{
AddLink(ref tssMap, ref LocusMap, filter, link);
}
}
return(filter.PostProcessLinkFilterType(tssMap, LocusMap));
}
}
